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Tungsten in PDB 3h1c: Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate

Enzymatic activity of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate

All present enzymatic activity of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate:
2.7.7.8; 3.1.26.12;

Protein crystallography data

The structure of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate, PDB code: 3h1c was solved by S.Nurmohamed, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 3.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 167.742, 262.887, 264.125, 90.00, 90.00, 90.00
R / Rfree (%) 27 / 30.4

Tungsten Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Tungsten atom in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate (pdb code 3h1c). This binding sites where shown within 5.0 Angstroms radius around Tungsten atom.
In total 21 binding sites of Tungsten where determined in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate, PDB code: 3h1c:
Jump to Tungsten binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Tungsten binding site 1 out of 21 in 3h1c

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Tungsten binding site 1 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 1 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W550

b:93.5
occ:0.50
W A:WO4550 0.0 93.5 0.5
O1 A:WO4550 2.0 87.4 0.5
O4 A:WO4550 2.0 88.2 0.5
O2 A:WO4550 2.0 84.5 0.5
O3 A:WO4550 2.0 86.9 0.5
O A:GLY436 3.6 56.0 1.0
N A:SER438 3.9 52.0 1.0
O3 A:WO4551 4.0 0.1 0.5
NE2 A:HIS403 4.2 44.9 1.0
NZ A:LYS494 4.3 37.2 1.0
CB A:SER438 4.4 50.2 1.0
CA A:SER437 4.5 55.0 1.0
OG A:SER438 4.5 48.7 1.0
CE1 A:HIS403 4.7 43.6 1.0
C A:SER437 4.7 53.6 1.0
CA A:SER438 4.7 50.6 1.0
C A:GLY436 4.7 54.4 1.0
CE A:LYS494 4.8 30.0 1.0
CD2 A:HIS403 4.8 44.1 1.0
N A:SER439 4.8 49.2 1.0
OG A:SER439 4.9 51.4 1.0

Tungsten binding site 2 out of 21 in 3h1c

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Tungsten binding site 2 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 2 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W551

b:0.5
occ:0.50
W A:WO4551 0.0 0.5 0.5
O1 A:WO4551 2.0 0.8 0.5
O3 A:WO4551 2.0 0.1 0.5
O2 A:WO4551 2.0 0.9 0.5
O4 A:WO4551 2.0 1.0 0.5
OD2 A:ASP508 4.1 73.1 1.0
OD2 A:ASP492 4.3 51.0 1.0
NZ A:LYS494 4.3 37.2 1.0
O2 A:WO4550 4.4 84.5 0.5
NE2 A:HIS403 4.4 44.9 1.0
CG A:ASP508 4.9 59.6 1.0

Tungsten binding site 3 out of 21 in 3h1c

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Tungsten binding site 3 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 3 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:W550

b:82.4
occ:0.50
W B:WO4550 0.0 82.4 0.5
O3 B:WO4550 2.0 73.4 0.5
O4 B:WO4550 2.0 77.4 0.5
O1 B:WO4550 2.0 72.0 0.5
O2 B:WO4550 2.0 74.3 0.5
O B:GLY436 3.7 42.9 1.0
N B:SER438 4.3 39.3 1.0
CA B:SER437 4.4 41.9 1.0
NE2 B:HIS403 4.5 52.1 1.0
O1 B:WO4551 4.6 93.5 0.5
CE1 B:HIS403 4.6 47.4 1.0
C B:GLY436 4.8 42.2 1.0
NZ B:LYS494 4.9 38.3 1.0
C B:SER437 4.9 39.2 1.0

Tungsten binding site 4 out of 21 in 3h1c

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Tungsten binding site 4 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 4 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:W551

b:97.7
occ:0.50
W B:WO4551 0.0 97.7 0.5
O2 B:WO4551 2.0 89.0 0.5
O4 B:WO4551 2.0 92.5 0.5
O3 B:WO4551 2.0 89.5 0.5
O1 B:WO4551 2.0 93.5 0.5
NH1 B:ARG399 4.0 70.9 1.0
NH2 B:ARG93 4.4 49.5 1.0
CZ B:ARG399 4.4 75.2 1.0
NE2 B:HIS403 4.5 52.1 1.0
OD2 B:ASP508 4.6 70.8 1.0
NH2 B:ARG399 4.8 70.1 1.0
CE1 B:HIS403 4.9 47.4 1.0

Tungsten binding site 5 out of 21 in 3h1c

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Tungsten binding site 5 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 5 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:W550

b:90.9
occ:0.50
W C:WO4550 0.0 90.9 0.5
O2 C:WO4550 2.0 80.3 0.5
O1 C:WO4550 2.0 85.7 0.5
O3 C:WO4550 2.0 89.8 0.5
O4 C:WO4550 2.0 84.9 0.5
O C:GLY436 3.4 62.0 1.0
OG C:SER438 4.4 51.1 1.0
N C:SER438 4.6 54.2 1.0
CA C:SER437 4.6 60.8 1.0
C C:GLY436 4.6 60.7 1.0
NH2 C:ARG399 4.7 87.9 1.0
CE1 C:HIS403 4.8 53.0 1.0
NZ C:LYS494 4.8 44.1 1.0
NE2 C:HIS403 5.0 55.3 1.0

Tungsten binding site 6 out of 21 in 3h1c

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Tungsten binding site 6 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 6 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:W550

b:93.6
occ:0.50
W G:WO4550 0.0 93.6 0.5
O2 G:WO4550 2.0 88.3 0.5
O1 G:WO4550 2.0 79.9 0.5
O4 G:WO4550 2.0 79.2 0.5
O3 G:WO4550 2.0 88.1 0.5
O G:GLY436 3.7 45.7 1.0
OG G:SER438 4.1 42.9 1.0
N G:SER438 4.2 39.9 1.0
CA G:SER437 4.2 44.4 1.0
NH2 G:ARG399 4.3 77.0 1.0
NE2 G:HIS403 4.4 42.3 1.0
C G:GLY436 4.6 44.1 1.0
C G:SER437 4.8 41.0 1.0
OD2 G:ASP486 4.8 75.1 1.0
OG G:SER437 4.8 54.3 1.0
NZ G:LYS494 4.9 40.1 1.0
N G:SER437 4.9 44.4 1.0
CB G:SER437 5.0 47.3 1.0

Tungsten binding site 7 out of 21 in 3h1c

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Tungsten binding site 7 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 7 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:W550

b:91.3
occ:0.50
W I:WO4550 0.0 91.3 0.5
O2 I:WO4550 2.0 90.4 0.5
O4 I:WO4550 2.0 89.8 0.5
O1 I:WO4550 2.0 91.2 0.5
O3 I:WO4550 2.0 90.5 0.5
OG I:SER438 4.2 47.9 1.0
NZ I:LYS494 4.3 27.1 1.0
N I:SER438 4.5 48.7 1.0
CA I:SER437 4.6 53.6 1.0
OG I:SER439 4.6 48.3 1.0
CE1 I:HIS403 4.7 52.5 1.0
NE2 I:HIS403 4.8 51.1 1.0
OG I:SER437 4.9 57.4 1.0
CE I:LYS494 4.9 26.5 1.0
O I:GLY436 4.9 57.9 1.0

Tungsten binding site 8 out of 21 in 3h1c

Go back to Tungsten Binding Sites List in 3h1c
Tungsten binding site 8 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 8 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
K:W550

b:88.7
occ:0.50
W K:WO4550 0.0 88.7 0.5
O2 K:WO4550 2.0 82.3 0.5
O1 K:WO4550 2.0 78.4 0.5
O3 K:WO4550 2.0 82.8 0.5
O4 K:WO4550 2.0 79.1 0.5
O K:GLY436 3.4 58.3 1.0
N K:SER438 4.2 47.2 1.0
CB K:SER438 4.4 45.2 1.0
C K:GLY436 4.6 55.7 1.0
O1 K:WO4551 4.6 99.6 0.5
NZ K:LYS494 4.8 34.1 1.0
CE1 K:HIS403 4.8 56.3 1.0
CA K:SER437 4.8 54.6 1.0
OD2 K:ASP486 4.8 66.2 1.0
CA K:SER438 4.9 45.1 1.0

Tungsten binding site 9 out of 21 in 3h1c

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Tungsten binding site 9 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 9 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
K:W551

b:0.7
occ:0.50
W K:WO4551 0.0 0.7 0.5
O1 K:WO4551 2.0 99.6 0.5
O3 K:WO4551 2.0 96.0 0.5
O4 K:WO4551 2.0 97.5 0.5
O2 K:WO4551 2.0 0.0 0.5
NH2 K:ARG93 4.2 64.4 1.0
OD2 K:ASP508 4.5 66.7 1.0
O2 K:WO4550 4.5 82.3 0.5
CE1 K:HIS403 4.8 56.3 1.0
CD K:ARG399 4.9 61.8 1.0
NE2 K:HIS403 4.9 51.5 1.0

Tungsten binding site 10 out of 21 in 3h1c

Go back to Tungsten Binding Sites List in 3h1c
Tungsten binding site 10 out of 21 in the Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 10 of Crystal Structure of Polynucleotide Phosphorylase (Pnpase) Core Bound to Rnase E and Tungstate within 5.0Å range:
probe atom residue distance (Å) B Occ
M:W550

b:0.7
occ:0.50
W M:WO4550 0.0 0.7 0.5
O4 M:WO4550 2.0 0.7 0.5
O1 M:WO4550 2.0 0.7 0.5
O2 M:WO4550 2.0 0.0 0.5
O3 M:WO4550 2.0 0.7 0.5
OG M:SER438 3.6 78.1 1.0
O4 M:WO4551 4.4 0.7 0.5
O M:GLY436 4.7 63.6 1.0
OD2 M:ASP486 4.7 52.8 1.0
CE1 M:HIS403 4.7 66.7 1.0
O M:SER437 4.8 81.9 1.0
CB M:SER438 4.9 75.9 1.0

Reference:

S.Nurmohamed, B.Vaidialingam, A.J.Callaghan, B.F.Luisi. Crystal Structure of Escherichia Coli Polynucleotide Phosphorylase Core Bound to Rnase E, Rna and Manganese: Implications For Catalytic Mechanism and Rna Degradosome Assembly J.Mol.Biol. V. 389 17 2009.
ISSN: ISSN 0022-2836
PubMed: 19327365
DOI: 10.1016/J.JMB.2009.03.051
Page generated: Wed Dec 16 02:34:48 2020

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