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Zinc in PDB 2qee: Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125

Protein crystallography data

The structure of Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125, PDB code: 2qee was solved by V.N.Malashkevich, R.Toro, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.65
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 121.995, 122.208, 127.582, 78.85, 78.95, 80.92
R / Rfree (%) 18.7 / 22.4

Other elements in 2qee:

The structure of Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 16 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125 (pdb code 2qee). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125, PDB code: 2qee:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 2qee

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Zinc binding site 1 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5021

b:36.3
occ:0.50
O A:HOH5312 1.7 42.6 1.0
OD1 A:ASP355 2.2 29.3 1.0
NE2 A:HIS26 2.2 22.2 1.0
NE2 A:HIS28 2.4 27.8 1.0
CG A:ASP355 2.9 33.9 1.0
OD2 A:ASP355 3.0 38.4 1.0
CD2 A:HIS28 3.1 29.5 1.0
CD2 A:HIS26 3.2 25.1 1.0
CE1 A:HIS26 3.2 28.8 1.0
CE1 A:HIS28 3.6 30.4 1.0
NE1 A:TRP325 4.3 26.1 1.0
CB A:ASP355 4.3 18.7 1.0
ND1 A:HIS26 4.3 30.3 1.0
CG A:HIS26 4.3 18.7 1.0
CG A:HIS28 4.3 27.5 1.0
CE A:MET258 4.4 38.4 1.0
ND1 A:HIS28 4.5 31.0 1.0
SD A:MET258 4.6 29.3 1.0
CA A:ASP355 4.8 17.0 1.0
CD1 A:TRP325 5.0 26.7 1.0

Zinc binding site 2 out of 12 in 2qee

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Zinc binding site 2 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5022

b:35.4
occ:0.50
O B:HOH5196 2.0 38.6 1.0
OD1 B:ASP355 2.0 30.0 1.0
NE2 B:HIS26 2.1 23.8 1.0
NE2 B:HIS28 2.3 30.6 1.0
CG B:ASP355 2.8 38.9 1.0
CD2 B:HIS28 2.9 26.7 1.0
OD2 B:ASP355 3.0 42.1 1.0
CE1 B:HIS26 3.0 30.4 1.0
CD2 B:HIS26 3.1 24.5 1.0
CE1 B:HIS28 3.5 28.4 1.0
ND1 B:HIS26 4.1 29.2 1.0
CG B:HIS28 4.2 26.9 1.0
CB B:ASP355 4.2 19.8 1.0
CG B:HIS26 4.2 21.0 1.0
NE1 B:TRP325 4.3 21.8 1.0
ND1 B:HIS28 4.4 25.7 1.0
O B:HOH5358 4.5 37.6 1.0
CE B:MET258 4.6 35.5 1.0
CA B:ASP355 4.7 18.4 1.0
SD B:MET258 4.7 27.3 1.0
CD1 B:TRP325 5.0 26.6 1.0

Zinc binding site 3 out of 12 in 2qee

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Zinc binding site 3 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


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 Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn5023

b:30.7
occ:0.50
O C:HOH5243 1.8 36.4 1.0
OD1 C:ASP355 2.1 26.4 1.0
NE2 C:HIS26 2.2 24.0 1.0
NE2 C:HIS28 2.3 26.5 1.0
CG C:ASP355 2.9 39.3 1.0
CD2 C:HIS28 2.9 28.2 1.0
CD2 C:HIS26 3.1 25.4 1.0
OD2 C:ASP355 3.1 35.8 1.0
CE1 C:HIS26 3.2 28.6 1.0
CE1 C:HIS28 3.4 29.9 1.0
CE C:MET258 4.1 35.6 1.0
CG C:HIS28 4.2 22.8 1.0
CB C:ASP355 4.2 19.3 1.0
CG C:HIS26 4.2 20.2 1.0
NH2 C:ARG170 4.3 18.4 0.5
ND1 C:HIS26 4.3 26.4 1.0
NE1 C:TRP325 4.3 21.9 1.0
ND1 C:HIS28 4.4 27.2 1.0
CA C:ASP355 4.7 15.9 1.0
SD C:MET258 4.8 24.6 1.0
O C:HOH5389 4.8 47.1 1.0
O C:HOH5076 5.0 27.6 1.0

Zinc binding site 4 out of 12 in 2qee

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Zinc binding site 4 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


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 Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn5024

b:36.7
occ:0.50
O D:HOH5117 1.8 39.5 1.0
OD1 D:ASP355 2.1 34.0 1.0
NE2 D:HIS26 2.1 25.3 1.0
NE2 D:HIS28 2.3 28.2 1.0
CD2 D:HIS28 3.0 30.5 1.0
CG D:ASP355 3.0 42.6 1.0
CD2 D:HIS26 3.1 27.3 1.0
CE1 D:HIS26 3.1 31.3 1.0
OD2 D:ASP355 3.3 42.7 1.0
CE1 D:HIS28 3.5 32.6 1.0
CE D:MET258 4.1 29.6 1.0
ND1 D:HIS26 4.2 30.3 1.0
CG D:HIS26 4.2 25.3 1.0
CG D:HIS28 4.3 26.5 1.0
NE1 D:TRP325 4.3 26.4 1.0
CB D:ASP355 4.4 23.7 1.0
ND1 D:HIS28 4.5 30.8 1.0
SD D:MET258 4.6 29.1 1.0
CA D:ASP355 4.7 19.8 1.0
O D:HOH5447 4.7 39.2 1.0
CD1 D:TRP325 5.0 26.7 1.0

Zinc binding site 5 out of 12 in 2qee

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Zinc binding site 5 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


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 Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn5025

b:35.3
occ:0.50
O E:HOH5317 1.9 36.1 1.0
OD1 E:ASP355 2.1 30.3 1.0
NE2 E:HIS26 2.2 28.3 1.0
NE2 E:HIS28 2.3 29.7 1.0
CG E:ASP355 2.9 42.6 1.0
CD2 E:HIS28 3.0 30.2 1.0
OD2 E:ASP355 3.1 38.5 1.0
CD2 E:HIS26 3.2 26.9 1.0
CE1 E:HIS26 3.2 31.9 1.0
CE1 E:HIS28 3.5 32.6 1.0
CE E:MET258 4.3 32.4 1.0
CG E:HIS28 4.3 24.9 1.0
ND1 E:HIS26 4.3 29.3 1.0
CB E:ASP355 4.3 22.2 1.0
NE1 E:TRP325 4.3 23.1 1.0
CG E:HIS26 4.3 21.3 1.0
ND1 E:HIS28 4.5 30.8 1.0
CA E:ASP355 4.8 18.8 1.0
SD E:MET258 4.8 25.5 1.0
CD1 E:TRP325 5.0 25.4 1.0

Zinc binding site 6 out of 12 in 2qee

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Zinc binding site 6 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


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 Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn5026

b:31.0
occ:0.50
O F:HOH5320 2.0 40.7 1.0
OD1 F:ASP355 2.0 27.4 1.0
NE2 F:HIS26 2.3 21.3 1.0
NE2 F:HIS28 2.3 27.5 1.0
CG F:ASP355 2.9 35.2 1.0
CD2 F:HIS28 2.9 30.1 1.0
OD2 F:ASP355 3.1 40.9 1.0
CD2 F:HIS26 3.1 22.1 1.0
CE1 F:HIS26 3.3 25.6 1.0
CE1 F:HIS28 3.5 33.9 1.0
O F:HOH5144 4.1 42.6 1.0
CG F:HIS28 4.2 26.0 1.0
CB F:ASP355 4.2 21.1 1.0
CG F:HIS26 4.3 17.1 1.0
ND1 F:HIS26 4.3 27.5 1.0
CE F:MET258 4.4 35.7 1.0
NE1 F:TRP325 4.4 22.0 1.0
ND1 F:HIS28 4.4 28.4 1.0
CA F:ASP355 4.6 16.5 1.0
SD F:MET258 4.8 29.4 1.0
OG1 F:THR143 5.0 19.9 1.0

Zinc binding site 7 out of 12 in 2qee

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Zinc binding site 7 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


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 Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn5027

b:40.9
occ:0.50
NE2 G:HIS26 2.1 36.4 1.0
O G:HOH5227 2.1 42.2 1.0
OD1 G:ASP355 2.1 31.1 1.0
NE2 G:HIS28 2.4 35.8 1.0
CG G:ASP355 2.9 44.6 1.0
CE1 G:HIS26 3.0 33.5 1.0
CD2 G:HIS26 3.1 30.2 1.0
CD2 G:HIS28 3.1 36.6 1.0
OD2 G:ASP355 3.1 39.7 1.0
CE1 G:HIS28 3.6 39.6 1.0
ND1 G:HIS26 4.1 34.7 1.0
CE G:MET258 4.1 38.1 1.0
CG G:HIS26 4.2 30.2 1.0
NE1 G:TRP325 4.3 28.8 1.0
CB G:ASP355 4.3 23.7 1.0
CG G:HIS28 4.3 37.4 1.0
ND1 G:HIS28 4.6 35.0 1.0
SD G:MET258 4.6 31.6 1.0
CA G:ASP355 4.8 22.7 1.0
OG1 G:THR143 5.0 22.6 1.0

Zinc binding site 8 out of 12 in 2qee

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Zinc binding site 8 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


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 Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn5028

b:31.3
occ:0.50
O H:HOH5394 2.0 39.8 1.0
OD1 H:ASP355 2.1 35.8 1.0
NE2 H:HIS26 2.2 23.4 1.0
NE2 H:HIS28 2.3 31.4 1.0
CG H:ASP355 2.9 43.5 1.0
CD2 H:HIS28 3.0 28.6 1.0
CD2 H:HIS26 3.1 23.6 1.0
OD2 H:ASP355 3.2 40.1 1.0
CE1 H:HIS26 3.2 30.7 1.0
CE1 H:HIS28 3.4 29.4 1.0
CG H:HIS28 4.2 28.5 1.0
CG H:HIS26 4.3 21.3 1.0
NE1 H:TRP325 4.3 21.2 1.0
ND1 H:HIS26 4.3 27.8 1.0
CB H:ASP355 4.3 21.8 1.0
ND1 H:HIS28 4.4 30.5 1.0
CE H:MET258 4.4 35.7 1.0
CA H:ASP355 4.8 18.3 1.0
SD H:MET258 4.8 26.8 1.0
CD1 H:TRP325 5.0 24.9 1.0
OG1 H:THR143 5.0 21.9 1.0

Zinc binding site 9 out of 12 in 2qee

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Zinc binding site 9 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


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 Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn5029

b:34.9
occ:0.50
O I:HOH5229 1.9 45.9 1.0
OD1 I:ASP355 2.0 32.5 1.0
NE2 I:HIS26 2.3 27.4 1.0
NE2 I:HIS28 2.4 35.0 1.0
CG I:ASP355 2.8 47.6 1.0
OD2 I:ASP355 3.0 41.3 1.0
CD2 I:HIS28 3.0 31.2 1.0
CD2 I:HIS26 3.2 27.9 1.0
CE1 I:HIS26 3.3 32.4 1.0
CE1 I:HIS28 3.5 37.1 1.0
CB I:ASP355 4.2 23.1 1.0
NE1 I:TRP325 4.2 21.7 1.0
CG I:HIS28 4.3 27.2 1.0
CG I:HIS26 4.4 25.5 1.0
ND1 I:HIS26 4.4 33.3 1.0
CE I:MET258 4.4 36.4 1.0
ND1 I:HIS28 4.5 26.9 1.0
SD I:MET258 4.7 29.5 1.0
CA I:ASP355 4.8 18.4 1.0
CD1 I:TRP325 4.9 23.6 1.0

Zinc binding site 10 out of 12 in 2qee

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Zinc binding site 10 out of 12 in the Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn5030

b:38.4
occ:0.50
O J:HOH5345 2.0 45.8 1.0
NE2 J:HIS26 2.1 35.8 1.0
OD1 J:ASP355 2.1 42.1 1.0
NE2 J:HIS28 2.2 44.8 1.0
CG J:ASP355 2.9 50.6 1.0
CE1 J:HIS26 3.0 27.8 1.0
CD2 J:HIS28 3.0 31.8 1.0
OD2 J:ASP355 3.1 44.1 1.0
CD2 J:HIS26 3.1 29.4 1.0
CE1 J:HIS28 3.3 39.3 1.0
CE J:MET258 3.9 36.3 1.0
ND1 J:HIS26 4.1 36.1 1.0
CG J:HIS26 4.2 25.6 1.0
CG J:HIS28 4.2 39.3 1.0
CB J:ASP355 4.3 29.5 1.0
NE1 J:TRP325 4.3 29.1 1.0
ND1 J:HIS28 4.3 37.6 1.0
SD J:MET258 4.8 32.3 1.0
CA J:ASP355 4.8 27.1 1.0

Reference:

V.N.Malashkevich, R.Toro, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Putative Amidohydrolase BH0493 From Bacillus Halodurans C-125. To Be Published.
Page generated: Wed Dec 16 03:50:14 2020

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