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Zinc in PDB 3a6l: E122Q Mutant Creatininase, Zn-Zn Type

Enzymatic activity of E122Q Mutant Creatininase, Zn-Zn Type

All present enzymatic activity of E122Q Mutant Creatininase, Zn-Zn Type:
3.5.2.10;

Protein crystallography data

The structure of E122Q Mutant Creatininase, Zn-Zn Type, PDB code: 3a6l was solved by Y.Nakajima, K.Yamashita, K.Ito, T.Yoshimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.400, 164.400, 164.600, 90.00, 90.00, 120.00
R / Rfree (%) 23.5 / 25.9

Other elements in 3a6l:

The structure of E122Q Mutant Creatininase, Zn-Zn Type also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the E122Q Mutant Creatininase, Zn-Zn Type (pdb code 3a6l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the E122Q Mutant Creatininase, Zn-Zn Type, PDB code: 3a6l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 3a6l

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Zinc binding site 1 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn300

b:26.1
occ:1.00
OD2 A:ASP45 2.0 22.8 1.0
OE1 A:GLU34 2.0 20.4 1.0
ND1 A:HIS120 2.2 23.3 1.0
CD A:GLU34 2.9 22.6 1.0
CL A:CL302 3.0 36.6 1.0
CE1 A:HIS120 3.0 21.0 1.0
O A:HOH1157 3.0 47.7 1.0
CG A:ASP45 3.1 21.9 1.0
OE2 A:GLU34 3.2 23.1 1.0
CG A:HIS120 3.3 25.4 1.0
OD1 A:ASP45 3.6 21.4 1.0
CB A:HIS120 3.8 24.4 1.0
CA A:HIS120 3.8 25.4 1.0
ZN A:ZN301 3.8 24.9 1.0
NE2 A:HIS120 4.2 26.3 1.0
CG A:GLU34 4.2 20.2 1.0
N A:TYR121 4.3 29.6 1.0
CB A:ASP45 4.3 22.3 1.0
NE2 A:GLN122 4.4 47.2 1.0
CD2 A:HIS120 4.4 23.3 1.0
CB A:GLU34 4.4 20.7 1.0
CE1 A:HIS36 4.5 15.9 1.0
C A:HIS120 4.5 27.2 1.0
CE1 A:HIS178 4.5 33.8 1.0
NE2 A:HIS36 4.6 12.8 1.0
O A:GLY119 4.6 21.0 1.0
ND1 A:HIS178 4.6 35.2 1.0
CB A:ALA32 4.8 19.8 1.0
N A:HIS120 5.0 21.5 1.0

Zinc binding site 2 out of 12 in 3a6l

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Zinc binding site 2 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:24.9
occ:1.00
OD1 A:ASP45 2.1 21.4 1.0
NE2 A:HIS36 2.1 12.8 1.0
OE2 A:GLU183 2.2 26.1 1.0
OE1 A:GLU183 2.6 24.9 1.0
CD A:GLU183 2.7 26.9 1.0
CG A:ASP45 3.1 21.9 1.0
CE1 A:HIS36 3.1 15.9 1.0
CD2 A:HIS36 3.1 16.7 1.0
CL A:CL302 3.3 36.6 1.0
OD2 A:ASP45 3.3 22.8 1.0
ZN A:ZN300 3.8 26.1 1.0
O A:HOH1274 4.0 28.5 1.0
CG1 A:VAL44 4.1 17.3 1.0
OE1 A:GLU34 4.1 20.4 1.0
ND1 A:HIS178 4.2 35.2 1.0
ND1 A:HIS36 4.2 17.7 1.0
CG A:GLU183 4.2 26.4 1.0
CG A:HIS36 4.2 19.1 1.0
CE1 A:HIS178 4.3 33.8 1.0
CB A:ASP45 4.4 22.3 1.0
O A:GLY119 4.4 21.0 1.0
N A:ASP45 4.5 20.5 1.0
CB A:VAL44 4.6 21.8 1.0
CA A:ASP45 4.7 21.8 1.0

Zinc binding site 3 out of 12 in 3a6l

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Zinc binding site 3 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn300

b:25.6
occ:1.00
OD2 B:ASP45 2.0 18.8 1.0
ND1 B:HIS120 2.1 23.1 1.0
OE1 B:GLU34 2.2 19.1 1.0
CL B:CL302 2.9 34.3 1.0
CE1 B:HIS120 3.0 24.8 1.0
CD B:GLU34 3.0 20.1 1.0
CG B:ASP45 3.2 22.8 1.0
CG B:HIS120 3.3 23.1 1.0
OE2 B:GLU34 3.3 22.2 1.0
CB B:HIS120 3.7 23.9 1.0
OD1 B:ASP45 3.7 27.6 1.0
CA B:HIS120 3.8 25.3 1.0
ZN B:ZN301 3.8 23.6 1.0
NE2 B:HIS120 4.1 26.3 1.0
N B:TYR121 4.2 29.0 1.0
CG B:GLU34 4.3 20.2 1.0
CD2 B:HIS120 4.3 24.6 1.0
CB B:ASP45 4.4 21.2 1.0
CB B:GLU34 4.4 17.0 1.0
C B:HIS120 4.5 27.0 1.0
CE1 B:HIS178 4.5 25.5 1.0
CE1 B:HIS36 4.6 23.0 1.0
O B:GLY119 4.6 22.2 1.0
ND1 B:HIS178 4.7 27.2 1.0
CB B:ALA32 4.7 18.5 1.0
NE2 B:HIS36 4.8 21.6 1.0
N B:HIS120 5.0 23.1 1.0

Zinc binding site 4 out of 12 in 3a6l

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Zinc binding site 4 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:23.6
occ:1.00
OD1 B:ASP45 2.1 27.6 1.0
OE2 B:GLU183 2.1 31.0 1.0
NE2 B:HIS36 2.2 21.6 1.0
CD B:GLU183 2.8 29.3 1.0
OE1 B:GLU183 2.8 30.5 1.0
CE1 B:HIS36 3.0 23.0 1.0
CL B:CL302 3.0 34.3 1.0
CG B:ASP45 3.1 22.8 1.0
CD2 B:HIS36 3.3 20.1 1.0
OD2 B:ASP45 3.4 18.8 1.0
ZN B:ZN300 3.8 25.6 1.0
O B:HOH1071 3.9 27.1 1.0
OE1 B:GLU34 4.1 19.1 1.0
ND1 B:HIS178 4.1 27.2 1.0
CG1 B:VAL44 4.1 21.7 1.0
ND1 B:HIS36 4.2 20.0 1.0
CE1 B:HIS178 4.2 25.5 1.0
CG B:GLU183 4.3 27.8 1.0
CG B:HIS36 4.4 21.1 1.0
O B:GLY119 4.4 22.2 1.0
CB B:ASP45 4.5 21.2 1.0
N B:ASP45 4.6 22.2 1.0
CB B:VAL44 4.6 20.0 1.0
CA B:ASP45 4.7 22.1 1.0

Zinc binding site 5 out of 12 in 3a6l

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Zinc binding site 5 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn300

b:29.3
occ:1.00
OD2 C:ASP45 2.0 23.2 1.0
ND1 C:HIS120 2.1 23.8 1.0
OE1 C:GLU34 2.2 24.6 1.0
CE1 C:HIS120 2.9 22.9 1.0
CD C:GLU34 3.0 25.4 1.0
CL C:CL302 3.0 39.2 1.0
CG C:ASP45 3.1 24.7 1.0
CG C:HIS120 3.3 23.7 1.0
OE2 C:GLU34 3.3 25.5 1.0
OD1 C:ASP45 3.6 22.7 1.0
CB C:HIS120 3.8 25.1 1.0
CA C:HIS120 3.8 25.3 1.0
ZN C:ZN301 3.9 26.1 1.0
NE2 C:HIS120 4.1 23.8 1.0
N C:TYR121 4.2 28.3 1.0
CG C:GLU34 4.3 23.9 1.0
CB C:ASP45 4.3 24.8 1.0
CD2 C:HIS120 4.3 24.2 1.0
CB C:GLU34 4.4 22.0 1.0
CE1 C:HIS36 4.5 21.2 1.0
C C:HIS120 4.5 27.0 1.0
O C:GLY119 4.5 22.6 1.0
CE1 C:HIS178 4.6 23.4 1.0
NE2 C:HIS36 4.6 21.3 1.0
CB C:ALA32 4.6 22.4 1.0
ND1 C:HIS178 4.8 27.2 1.0
N C:HIS120 5.0 23.5 1.0

Zinc binding site 6 out of 12 in 3a6l

Go back to Zinc Binding Sites List in 3a6l
Zinc binding site 6 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:26.1
occ:1.00
OE1 C:GLU183 2.1 28.0 1.0
NE2 C:HIS36 2.2 21.3 1.0
OD1 C:ASP45 2.2 22.7 1.0
OE2 C:GLU183 2.6 27.9 1.0
CD C:GLU183 2.7 29.4 1.0
CG C:ASP45 3.1 24.7 1.0
CE1 C:HIS36 3.1 21.2 1.0
CD2 C:HIS36 3.2 21.4 1.0
CL C:CL302 3.2 39.2 1.0
OD2 C:ASP45 3.3 23.2 1.0
ZN C:ZN300 3.9 29.3 1.0
O C:HOH1152 3.9 37.9 1.0
CG1 C:VAL44 4.0 23.5 1.0
OE1 C:GLU34 4.1 24.6 1.0
CG C:GLU183 4.1 28.6 1.0
ND1 C:HIS36 4.2 21.7 1.0
ND1 C:HIS178 4.3 27.2 1.0
CG C:HIS36 4.3 22.1 1.0
CE1 C:HIS178 4.3 23.4 1.0
CB C:ASP45 4.4 24.8 1.0
O C:GLY119 4.5 22.6 1.0
N C:ASP45 4.6 23.1 1.0
CB C:VAL44 4.6 25.4 1.0
CA C:ASP45 4.7 24.6 1.0

Zinc binding site 7 out of 12 in 3a6l

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Zinc binding site 7 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn300

b:25.8
occ:1.00
OD2 D:ASP45 2.1 16.6 1.0
OE1 D:GLU34 2.1 27.1 1.0
ND1 D:HIS120 2.2 25.4 1.0
CE1 D:HIS120 3.0 27.7 1.0
CD D:GLU34 3.0 24.3 1.0
CL D:CL302 3.0 34.6 1.0
CG D:ASP45 3.2 20.9 1.0
CG D:HIS120 3.3 25.6 1.0
OE2 D:GLU34 3.4 25.7 1.0
OD1 D:ASP45 3.7 24.2 1.0
CB D:HIS120 3.8 26.2 1.0
CA D:HIS120 3.8 26.9 1.0
ZN D:ZN301 3.8 25.7 1.0
NE2 D:HIS120 4.2 25.7 1.0
CG D:GLU34 4.3 21.1 1.0
N D:TYR121 4.3 28.6 1.0
CD2 D:HIS120 4.4 28.0 1.0
CB D:ASP45 4.4 20.9 1.0
CB D:GLU34 4.4 20.0 1.0
CE1 D:HIS36 4.4 25.7 1.0
CE1 D:HIS178 4.5 22.9 1.0
C D:HIS120 4.5 27.2 1.0
OE1 D:GLN122 4.5 50.7 1.0
O D:GLY119 4.5 24.3 1.0
CB D:ALA32 4.6 17.2 1.0
NE2 D:HIS36 4.7 23.0 1.0
ND1 D:HIS178 4.7 24.0 1.0
N D:HIS120 5.0 25.3 1.0

Zinc binding site 8 out of 12 in 3a6l

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Zinc binding site 8 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:25.7
occ:1.00
NE2 D:HIS36 2.1 23.0 1.0
OD1 D:ASP45 2.1 24.2 1.0
OE1 D:GLU183 2.2 27.9 1.0
OE2 D:GLU183 2.7 30.6 1.0
CD D:GLU183 2.7 29.2 1.0
CE1 D:HIS36 2.9 25.7 1.0
CL D:CL302 3.1 34.6 1.0
CG D:ASP45 3.1 20.9 1.0
CD2 D:HIS36 3.2 23.4 1.0
OD2 D:ASP45 3.4 16.6 1.0
ZN D:ZN300 3.8 25.8 1.0
O D:HOH1457 3.9 37.1 1.0
ND1 D:HIS178 4.1 24.0 1.0
ND1 D:HIS36 4.1 23.2 1.0
CE1 D:HIS178 4.2 22.9 1.0
CG D:GLU183 4.2 27.9 1.0
OE1 D:GLU34 4.2 27.1 1.0
CG D:HIS36 4.3 23.1 1.0
CG1 D:VAL44 4.3 21.2 1.0
O D:GLY119 4.4 24.3 1.0
CB D:ASP45 4.5 20.9 1.0
N D:ASP45 4.6 23.8 1.0
CB D:VAL44 4.7 21.6 1.0
CA D:ASP45 4.7 22.7 1.0
O D:HOH1420 4.8 50.0 1.0

Zinc binding site 9 out of 12 in 3a6l

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Zinc binding site 9 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn300

b:26.1
occ:1.00
OD2 E:ASP45 2.0 22.5 1.0
OE1 E:GLU34 2.1 24.4 1.0
ND1 E:HIS120 2.2 25.1 1.0
CE1 E:HIS120 2.9 23.0 1.0
CL E:CL302 3.0 33.4 1.0
CD E:GLU34 3.0 26.7 1.0
CG E:ASP45 3.1 22.2 1.0
CG E:HIS120 3.3 25.0 1.0
OE2 E:GLU34 3.4 26.0 1.0
OD1 E:ASP45 3.6 18.4 1.0
ZN E:ZN301 3.8 25.0 1.0
CA E:HIS120 3.8 26.9 1.0
CB E:HIS120 3.8 25.3 1.0
NE2 E:HIS120 4.1 25.2 1.0
NE2 E:GLN122 4.2 46.7 1.0
CB E:ASP45 4.3 21.2 1.0
CG E:GLU34 4.3 25.6 1.0
CD2 E:HIS120 4.3 24.0 1.0
N E:TYR121 4.4 30.0 1.0
CE1 E:HIS178 4.4 28.6 1.0
NE2 E:HIS36 4.4 19.6 1.0
CB E:GLU34 4.5 25.0 1.0
CE1 E:HIS36 4.5 21.2 1.0
O E:GLY119 4.5 25.9 1.0
C E:HIS120 4.5 28.8 1.0
ND1 E:HIS178 4.5 30.6 1.0
CB E:ALA32 4.6 18.4 1.0
N E:HIS120 5.0 26.2 1.0

Zinc binding site 10 out of 12 in 3a6l

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Zinc binding site 10 out of 12 in the E122Q Mutant Creatininase, Zn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of E122Q Mutant Creatininase, Zn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:25.0
occ:1.00
OD1 E:ASP45 2.0 18.4 1.0
NE2 E:HIS36 2.2 19.6 1.0
OE2 E:GLU183 2.2 27.5 1.0
OE1 E:GLU183 2.6 26.8 1.0
CD E:GLU183 2.7 28.6 1.0
CG E:ASP45 3.0 22.2 1.0
CD2 E:HIS36 3.1 21.3 1.0
CL E:CL302 3.2 33.4 1.0
CE1 E:HIS36 3.2 21.2 1.0
OD2 E:ASP45 3.3 22.5 1.0
O E:HOH1163 3.8 28.2 1.0
ZN E:ZN300 3.8 26.1 1.0
CG1 E:VAL44 3.9 24.9 1.0
ND1 E:HIS178 4.1 30.6 1.0
CE1 E:HIS178 4.1 28.6 1.0
CG E:GLU183 4.2 27.8 1.0
OE1 E:GLU34 4.2 24.4 1.0
CG E:HIS36 4.3 21.1 1.0
ND1 E:HIS36 4.3 23.8 1.0
CB E:ASP45 4.4 21.2 1.0
O E:GLY119 4.4 25.9 1.0
N E:ASP45 4.5 23.4 1.0
CB E:VAL44 4.6 27.8 1.0
CA E:ASP45 4.6 22.3 1.0

Reference:

K.Yamashita, Y.Nakajima, H.Matsushita, Y.Nishiya, R.Yamazawa, Y.F.Wu, F.Matsubara, H.Oyama, K.Ito, T.Yoshimoto. Substitution of GLU122 By Glutamine Revealed the Function of the Second Water Molecule As A Proton Donor in the Binuclear Metal Enzyme Creatininase J.Mol.Biol. V. 396 1081 2010.
ISSN: ISSN 0022-2836
PubMed: 20043918
DOI: 10.1016/J.JMB.2009.12.045
Page generated: Wed Dec 16 04:06:29 2020

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