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Tungsten in PDB 9bem: Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound

Protein crystallography data

The structure of Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound, PDB code: 9bem was solved by D.Zhou, J.P.Rose, L.Chen, B.C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.81 / 2.26
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.751, 74.751, 156.584, 90, 90, 90
R / Rfree (%) 17.8 / 22.7

Tungsten Binding Sites:

The binding sites of Tungsten atom in the Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound (pdb code 9bem). This binding sites where shown within 5.0 Angstroms radius around Tungsten atom.
In total 7 binding sites of Tungsten where determined in the Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound, PDB code: 9bem:
Jump to Tungsten binding site number: 1; 2; 3; 4; 5; 6; 7;

Tungsten binding site 1 out of 7 in 9bem

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Tungsten binding site 1 out of 7 in the Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 1 of Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:W102

b:30.5
occ:0.75
 W A:WO4102 0.0 30.5 0.8
O4 A:WO4102 2.0 23.5 0.8
O3 A:WO4102 2.0 26.3 0.8
O1 A:WO4102 2.0 27.6 0.8
O2 A:WO4102 2.0 19.4 0.8
CG A:LYS60 3.7 23.1 1.0
O A:SER4 4.0 27.4 1.0
N C:SER40 4.0 19.3 1.0
NZ A:LYS60 4.0 16.3 1.0
O B:HOH216 4.0 23.7 1.0
N A:ALA61 4.0 21.9 1.0
CB C:ILE39 4.0 20.7 1.0
OG C:SER43 4.1 33.6 1.0
CG A:ARG6 4.1 25.4 1.0
N A:ARG6 4.1 22.8 1.0
CG2 C:ILE39 4.1 20.1 1.0
CA A:ALA5 4.2 22.5 1.0
CA C:ILE39 4.3 23.9 1.0
C A:SER4 4.4 24.7 1.0
CE A:LYS60 4.4 20.2 1.0
OG A:SER4 4.4 25.9 1.0
OG C:SER40 4.4 22.9 1.0
CB A:ALA61 4.5 19.4 1.0
N A:ALA5 4.6 23.2 1.0
CA A:LYS60 4.6 20.2 1.0
CB C:SER40 4.7 21.1 1.0
C C:ILE39 4.7 21.5 1.0
CD A:LYS60 4.7 24.1 1.0
C A:ALA5 4.7 23.7 1.0
CB A:LYS60 4.8 19.9 1.0
CB A:SER4 4.8 21.9 1.0
C A:LYS60 4.8 21.0 1.0
CB C:SER43 4.9 24.4 1.0
CA A:ALA61 4.9 19.3 1.0
CB A:ARG6 4.9 20.8 1.0
CA C:SER40 5.0 22.8 1.0
NE A:ARG6 5.0 27.7 1.0

Tungsten binding site 2 out of 7 in 9bem

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Tungsten binding site 2 out of 7 in the Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 2 of Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:W101

b:38.0
occ:0.62
 W B:WO4101 0.0 38.0 0.6
O4 B:WO4101 2.0 8.6 0.6
O2 B:WO4101 2.0 17.6 0.6
O1 B:WO4101 2.1 16.0 0.6
O3 B:WO4101 2.1 18.1 0.6
CG2 B:VAL21 3.8 21.1 1.0
CG2 C:VAL21 3.9 28.5 1.0
ND2 C:ASN22 4.3 21.8 1.0
CG2 E:VAL21 4.3 20.9 1.0
ND2 B:ASN22 4.4 19.4 1.0
ND2 E:ASN22 4.4 19.4 1.0
N B:ASN22 4.4 20.5 1.0
N B:VAL21 4.6 23.5 1.0
CB B:ASN22 4.6 23.6 1.0
N C:ASN22 4.7 24.2 1.0
N E:ASN22 4.7 24.3 1.0
CB E:ASN22 4.7 23.1 1.0
CB C:ASN22 4.7 22.7 1.0
N C:VAL21 4.8 27.1 1.0
N B:ALA20 4.9 20.6 1.0
CG C:ASN22 5.0 23.8 1.0
CG B:ASN22 5.0 23.7 1.0

Tungsten binding site 3 out of 7 in 9bem

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Tungsten binding site 3 out of 7 in the Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 3 of Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:W102

b:27.6
occ:0.70
 W B:WO4102 0.0 27.6 0.7
O2 B:WO4102 2.0 20.7 0.7
O4 B:WO4102 2.0 18.9 0.7
O3 B:WO4102 2.0 25.7 0.7
O1 B:WO4102 2.0 22.2 0.7
CG B:LYS60 3.8 25.8 1.0
N F:SER40 3.9 12.9 1.0
O B:SER4 3.9 28.8 1.0
NZ B:LYS60 4.0 22.3 1.0
N B:ALA61 4.0 20.4 1.0
CG2 F:ILE39 4.1 23.1 1.0
O B:HOH224 4.1 18.5 1.0
CB F:ILE39 4.1 19.5 1.0
CA B:ALA5 4.1 21.0 1.0
N B:ARG6 4.1 22.5 1.0
CG B:ARG6 4.2 27.1 1.0
OG B:SER4 4.3 17.6 1.0
CA F:ILE39 4.3 20.0 1.0
C B:SER4 4.3 24.9 1.0
OG F:SER40 4.4 23.4 1.0
N B:ALA5 4.5 21.5 1.0
CE B:LYS60 4.5 19.3 1.0
CA B:LYS60 4.6 18.7 1.0
CB B:ALA61 4.6 16.6 1.0
OG F:SER43 4.6 31.6 1.0
C B:ALA5 4.6 22.5 1.0
CB F:SER40 4.6 22.6 1.0
C F:ILE39 4.7 22.0 1.0
CB B:LYS60 4.7 19.2 1.0
CB B:SER4 4.8 20.8 1.0
C B:LYS60 4.8 20.6 1.0
CD B:LYS60 4.8 18.2 1.0
CB F:SER43 4.8 21.7 1.0
CA F:SER40 4.9 19.9 1.0
NE B:ARG6 4.9 29.3 1.0
CA B:ALA61 4.9 19.7 1.0

Tungsten binding site 4 out of 7 in 9bem

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Tungsten binding site 4 out of 7 in the Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 4 of Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:W101

b:29.9
occ:0.70
 W C:WO4101 0.0 29.9 0.7
O3 C:WO4101 2.0 20.6 0.7
O4 C:WO4101 2.0 21.9 0.7
O2 C:WO4101 2.0 19.3 0.7
O1 C:WO4101 2.0 19.6 0.7
CG C:LYS60 3.7 19.3 1.0
NZ C:LYS60 3.9 22.5 1.0
CG2 A:ILE39 4.0 20.1 1.0
O C:SER4 4.0 19.2 1.0
N A:SER40 4.0 20.0 1.0
CB A:ILE39 4.0 19.4 1.0
N C:ALA61 4.1 20.8 1.0
OG A:SER43 4.1 32.5 1.0
CG C:ARG6 4.1 25.8 1.0
N C:ARG6 4.2 26.2 1.0
CA C:ALA5 4.2 21.6 1.0
CA A:ILE39 4.3 21.6 1.0
OG C:SER4 4.3 18.5 1.0
C C:SER4 4.4 20.9 1.0
O D:HOH208 4.4 18.3 1.0
CE C:LYS60 4.4 19.1 1.0
OG A:SER40 4.5 24.3 1.0
N C:ALA5 4.5 23.0 1.0
CB C:ALA61 4.6 17.5 1.0
CA C:LYS60 4.7 20.2 1.0
C C:ALA5 4.7 21.2 1.0
CD C:LYS60 4.7 23.9 1.0
C A:ILE39 4.7 23.9 1.0
CB A:SER40 4.7 21.7 1.0
CB C:LYS60 4.8 23.3 1.0
CB C:SER4 4.8 19.5 1.0
CB C:ARG6 4.9 29.0 1.0
C C:LYS60 4.9 22.5 1.0
CB A:SER43 4.9 25.7 1.0
CA C:ALA61 5.0 18.6 1.0

Tungsten binding site 5 out of 7 in 9bem

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Tungsten binding site 5 out of 7 in the Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 5 of Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:W101

b:29.6
occ:0.79
 W D:WO4101 0.0 29.6 0.8
O1 D:WO4101 2.0 16.3 0.8
O3 D:WO4101 2.0 21.5 0.8
O2 D:WO4101 2.0 20.2 0.8
O4 D:WO4101 2.0 21.8 0.8
O D:HOH205 3.7 18.9 1.0
CG D:LYS60 3.7 17.1 1.0
O D:SER4 3.7 27.8 1.0
NZ D:LYS60 4.0 18.5 1.0
N D:ALA61 4.0 17.9 1.0
N E:SER40 4.0 16.9 1.0
CG2 E:ILE39 4.1 18.1 1.0
CB E:ILE39 4.1 19.7 1.0
CA D:ALA5 4.1 23.4 1.0
OG D:SER4 4.2 22.1 1.0
C D:SER4 4.2 26.7 1.0
N D:ARG6 4.2 22.8 1.0
CG D:ARG6 4.3 18.5 1.0
CA E:ILE39 4.3 17.4 1.0
OG E:SER43 4.4 24.9 1.0
N D:ALA5 4.4 23.1 1.0
CE D:LYS60 4.4 19.9 1.0
CB D:ALA61 4.5 18.3 1.0
OG E:SER40 4.5 20.5 1.0
CB D:SER4 4.7 25.9 1.0
CA D:LYS60 4.7 18.7 1.0
C D:ALA5 4.7 21.0 1.0
CD D:LYS60 4.7 19.1 1.0
CB E:SER40 4.7 21.5 1.0
C E:ILE39 4.7 18.1 1.0
CB D:LYS60 4.8 18.4 1.0
C D:LYS60 4.9 20.7 1.0
CA D:ALA61 4.9 19.9 1.0
CB E:SER43 4.9 20.8 1.0

Tungsten binding site 6 out of 7 in 9bem

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Tungsten binding site 6 out of 7 in the Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 6 of Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:W101

b:30.6
occ:0.76
 W E:WO4101 0.0 30.6 0.8
O2 E:WO4101 2.0 19.9 0.8
O3 E:WO4101 2.0 19.2 0.8
O4 E:WO4101 2.0 28.3 0.8
O1 E:WO4101 2.0 26.9 0.8
O E:HOH202 3.6 26.5 1.0
O E:SER4 3.7 31.7 1.0
CG E:LYS60 3.9 23.1 1.0
N D:SER40 4.0 18.9 1.0
NZ E:LYS60 4.1 19.7 1.0
N E:ALA61 4.1 20.1 1.0
CG2 D:ILE39 4.1 21.7 1.0
CB D:ILE39 4.1 24.0 1.0
OG D:SER43 4.1 32.6 1.0
N E:ARG6 4.1 24.0 1.0
CA E:ALA5 4.2 26.6 1.0
C E:SER4 4.3 32.4 1.0
CG E:ARG6 4.3 23.6 1.0
CA D:ILE39 4.3 23.7 1.0
CB E:ALA61 4.4 19.2 1.0
OG E:SER4 4.4 25.6 1.0
OG D:SER40 4.5 29.0 1.0
N E:ALA5 4.5 31.3 1.0
CE E:LYS60 4.5 23.0 1.0
C E:ALA5 4.6 29.4 1.0
C D:ILE39 4.7 21.8 1.0
CB D:SER40 4.7 22.5 1.0
CA E:LYS60 4.7 22.5 1.0
CB E:SER4 4.8 26.4 1.0
CA E:ALA61 4.9 20.7 1.0
CD E:LYS60 4.9 19.6 1.0
CB E:LYS60 4.9 18.1 1.0
C E:LYS60 4.9 18.5 1.0
CB D:SER43 5.0 28.7 1.0
CA D:SER40 5.0 25.8 1.0

Tungsten binding site 7 out of 7 in 9bem

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Tungsten binding site 7 out of 7 in the Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound


Mono view


Stereo pair view

A full contact list of Tungsten with other atoms in the W binding site number 7 of Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:W101

b:31.0
occ:0.70
 W F:WO4101 0.0 31.0 0.7
O2 F:WO4101 2.0 26.7 0.7
O4 F:WO4101 2.0 19.2 0.7
O3 F:WO4101 2.0 22.7 0.7
O1 F:WO4101 2.0 26.0 0.7
CG F:LYS60 3.7 21.6 1.0
N B:SER40 4.0 22.0 1.0
O F:SER4 4.0 25.9 1.0
N F:ALA61 4.0 19.5 1.0
CA F:ALA5 4.1 27.1 1.0
CB B:ILE39 4.1 18.6 1.0
N F:ARG6 4.1 24.7 1.0
NZ F:LYS60 4.1 20.7 1.0
CG2 B:ILE39 4.1 18.9 1.0
CG F:ARG6 4.1 28.0 1.0
CA B:ILE39 4.3 18.1 1.0
C F:SER4 4.4 26.8 1.0
O B:HOH211 4.4 23.3 1.0
OG F:SER4 4.4 20.9 1.0
OG B:SER40 4.4 23.0 1.0
N F:ALA5 4.5 22.9 1.0
CE F:LYS60 4.5 18.0 1.0
CA F:LYS60 4.5 21.4 1.0
CB F:ALA61 4.6 19.0 1.0
C F:ALA5 4.6 24.9 1.0
OG B:SER43 4.6 31.6 1.0
CB B:SER40 4.7 21.5 1.0
CB F:LYS60 4.7 20.5 1.0
C B:ILE39 4.7 21.9 1.0
CD F:LYS60 4.7 19.8 1.0
C F:LYS60 4.8 18.3 1.0
CB F:SER4 4.9 26.3 1.0
CB B:SER43 4.9 19.2 1.0
CA F:ALA61 4.9 17.8 1.0
CB F:ARG6 4.9 21.8 1.0
CA B:SER40 5.0 21.3 1.0

Reference:

D.Zhou, J.P.Rose, L.Chen, B.C.Wang. Tungstate Binding Protein (Tungbindin) From Eubacterium Limosum with Seven Tungstates Bound To Be Published.
Page generated: Sat Oct 12 16:33:50 2024

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