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Zinc in PDB 2gpy: Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans

Protein crystallography data

The structure of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans, PDB code: 2gpy was solved by U.A.Ramagopal, Y.V.Patskovsky, S.C.Almo, S.K.Burley, New York Sgxresearch Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.44 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.567, 62.807, 137.746, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans (pdb code 2gpy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans, PDB code: 2gpy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 2gpy

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Zinc binding site 1 out of 9 in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:41.7
occ:0.75
OE1 A:GLU29 1.8 44.8 1.0
NE2 A:HIS97 2.0 36.3 1.0
O A:HOH373 2.0 46.1 1.0
OE1 A:GLU93 2.4 40.2 0.5
CD A:GLU29 2.6 46.3 1.0
CE1 A:HIS97 2.8 32.3 1.0
OE2 A:GLU29 2.8 44.2 1.0
CD2 A:HIS97 3.1 36.8 1.0
CD A:GLU93 3.2 38.6 0.5
CG A:GLU93 3.3 37.8 0.5
ND1 A:HIS97 3.9 36.4 1.0
CG A:GLU29 4.0 46.5 1.0
CG A:HIS97 4.1 35.2 1.0
OE2 A:GLU93 4.4 37.7 0.5
CB A:GLU29 4.7 45.0 1.0
O A:HOH346 4.8 40.9 1.0
CB A:GLU93 4.9 36.9 0.5
OE2 A:GLU93 4.9 39.6 0.5
OH A:TYR22 5.0 33.1 1.0

Zinc binding site 2 out of 9 in 2gpy

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Zinc binding site 2 out of 9 in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:34.1
occ:0.40
O A:HOH319 2.2 44.9 1.0
OE1 A:GLN116 3.5 59.8 1.0
OD2 A:ASP113 3.9 56.7 1.0
CB A:ASP113 3.9 55.8 1.0
CG A:ASP113 4.4 56.5 1.0
CD A:GLN116 4.7 57.5 1.0

Zinc binding site 3 out of 9 in 2gpy

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Zinc binding site 3 out of 9 in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans within 5.0Å range:

Zinc binding site 4 out of 9 in 2gpy

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Zinc binding site 4 out of 9 in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:44.8
occ:0.40
OD1 A:ASP206 2.0 41.9 1.0
CG A:ASP206 2.9 41.9 1.0
OD2 A:ASP206 3.1 43.4 1.0
CB A:ASP206 4.2 42.0 1.0
CA A:ASP206 4.5 41.6 1.0
N A:ASP206 4.8 42.0 1.0
O A:GLY205 4.9 42.0 1.0
C A:GLY205 5.0 42.2 1.0

Zinc binding site 5 out of 9 in 2gpy

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Zinc binding site 5 out of 9 in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:41.0
occ:0.75
OD1 B:ASP206 2.1 38.7 1.0
CG B:ASP206 2.9 38.0 1.0
OD2 B:ASP206 2.9 36.1 1.0
O B:HOH416 4.2 46.9 1.0
CB B:ASP206 4.3 38.9 1.0
CB B:ASP39 4.6 43.0 1.0
CG B:ASP39 4.8 42.8 1.0
CA B:ASP206 4.8 39.4 1.0
MG B:MG301 4.8 35.8 1.0
OD1 B:ASP39 5.0 44.3 1.0
N B:ASP206 5.0 40.1 1.0

Zinc binding site 6 out of 9 in 2gpy

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Zinc binding site 6 out of 9 in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:42.1
occ:0.75
NE2 B:HIS31 2.2 41.4 1.0
CD2 B:HIS31 3.1 39.9 1.0
CE1 B:HIS31 3.2 41.0 1.0
O B:HOH379 3.3 50.5 1.0
CG B:HIS31 4.3 41.2 1.0
ND1 B:HIS31 4.3 40.5 1.0
O B:HOH411 4.9 46.3 1.0
O B:HOH413 5.0 52.7 1.0

Zinc binding site 7 out of 9 in 2gpy

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Zinc binding site 7 out of 9 in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:38.8
occ:0.75
NE2 B:HIS194 2.1 37.2 1.0
OD1 B:ASP144 2.1 45.8 1.0
O B:HOH394 2.1 29.3 1.0
CE1 B:HIS194 2.8 37.6 1.0
CG B:ASP144 2.9 41.7 1.0
OD2 B:ASP144 3.2 40.5 1.0
CD2 B:HIS194 3.2 38.0 1.0
ND1 B:HIS194 4.0 39.0 1.0
CG B:HIS194 4.2 39.5 1.0
CB B:ASP144 4.3 38.5 1.0
CA B:ASP144 4.6 38.2 1.0
CD1 B:PHE143 4.7 35.1 1.0
CZ3 B:TRP190 4.9 50.7 1.0
CE1 B:PHE143 4.9 36.0 1.0

Zinc binding site 8 out of 9 in 2gpy

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Zinc binding site 8 out of 9 in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn309

b:45.7
occ:0.40
NE2 B:HIS97 2.0 37.4 1.0
CE1 B:HIS97 2.4 32.7 1.0
OE1 B:GLU29 2.4 50.2 1.0
OE2 B:GLU93 2.5 48.4 1.0
CD2 B:HIS97 3.2 35.1 1.0
CD B:GLU29 3.3 48.5 1.0
CD B:GLU93 3.4 47.5 1.0
O B:HOH365 3.5 56.2 1.0
OE2 B:GLU29 3.5 49.4 1.0
CG B:GLU93 3.6 40.2 1.0
ND1 B:HIS97 3.7 38.3 1.0
O B:HOH330 3.7 44.4 1.0
CG B:HIS97 4.1 35.4 1.0
OE1 B:GLU93 4.4 48.9 1.0
CG B:GLU29 4.7 44.9 1.0

Zinc binding site 9 out of 9 in 2gpy

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Zinc binding site 9 out of 9 in the Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn310

b:55.6
occ:0.40
ND1 B:HIS48 2.0 38.8 1.0
CE1 B:HIS48 2.8 38.4 1.0
OD1 A:ASP198 3.0 45.6 1.0
CG B:HIS48 3.1 37.5 1.0
NZ B:LYS51 3.2 49.1 1.0
CE B:LYS51 3.6 47.8 1.0
CB B:HIS48 3.6 38.5 1.0
CG A:ASP198 3.6 42.5 1.0
O B:HOH349 3.6 38.6 1.0
OD2 A:ASP198 3.8 46.0 1.0
CA B:HIS48 3.8 38.1 1.0
CD B:LYS51 3.9 44.7 1.0
NE2 B:HIS48 4.0 36.3 1.0
CD2 B:HIS48 4.2 37.4 1.0
N B:HIS48 4.5 37.1 1.0
CB A:ASP198 4.7 40.7 1.0
CB A:ARG200 4.9 41.4 1.0
CG B:LYS51 5.0 42.6 1.0
O A:ASP198 5.0 40.1 1.0

Reference:

U.A.Ramagopal, Y.V.Patskovsky, S.C.Almo. Crystal Structure of Putative O-Methyltransferase From Bacillus Halodurans To Be Published.
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