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Zinc in PDB 3a6k: The E122Q Mutant Creatininase, Mn-Zn Type

Enzymatic activity of The E122Q Mutant Creatininase, Mn-Zn Type

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

Protein crystallography data

The structure of The E122Q Mutant Creatininase, Mn-Zn Type, PDB code: 3a6k 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 / 2.20
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 164.200, 164.200, 164.700, 90.00, 90.00, 120.00
R / Rfree (%) 20.7 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the The E122Q Mutant Creatininase, Mn-Zn Type (pdb code 3a6k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The E122Q Mutant Creatininase, Mn-Zn Type, PDB code: 3a6k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3a6k

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Zinc binding site 1 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The E122Q Mutant Creatininase, Mn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:37.2
occ:1.00
OE2 A:GLU183 2.0 44.4 1.0
NE2 A:HIS36 2.1 33.2 1.0
OD1 A:ASP45 2.1 30.6 1.0
CD A:GLU183 2.7 46.6 1.0
OE1 A:GLU183 2.7 47.3 1.0
CE1 A:HIS36 2.9 34.8 1.0
CL A:CL302 3.0 46.6 1.0
CG A:ASP45 3.0 31.2 1.0
CD2 A:HIS36 3.2 32.6 1.0
OD2 A:ASP45 3.2 32.8 1.0
MN A:MN300 3.7 40.7 1.0
O A:HOH1141 4.0 37.2 1.0
ND1 A:HIS178 4.1 51.0 1.0
ND1 A:HIS36 4.1 35.8 1.0
CG A:GLU183 4.1 45.6 1.0
CE1 A:HIS178 4.2 48.9 1.0
CG1 A:VAL44 4.2 31.4 1.0
OE1 A:GLU34 4.2 39.2 1.0
CG A:HIS36 4.3 36.7 1.0
CB A:ASP45 4.4 31.5 1.0
O A:GLY119 4.5 35.9 1.0
N A:ASP45 4.6 34.0 1.0
CB A:VAL44 4.6 34.8 1.0
CA A:ASP45 4.8 32.9 1.0

Zinc binding site 2 out of 6 in 3a6k

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Zinc binding site 2 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

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

b:33.0
occ:1.00
OD1 B:ASP45 2.0 23.9 1.0
OE1 B:GLU183 2.2 40.9 1.0
NE2 B:HIS36 2.2 29.9 1.0
OE2 B:GLU183 2.6 39.4 1.0
CD B:GLU183 2.7 39.4 1.0
CG B:ASP45 3.0 25.9 1.0
CL B:CL302 3.1 49.6 1.0
CD2 B:HIS36 3.1 31.7 1.0
CE1 B:HIS36 3.2 32.3 1.0
OD2 B:ASP45 3.2 27.2 1.0
MN B:MN300 3.7 39.6 1.0
O B:HOH1095 4.0 35.2 1.0
ND1 B:HIS178 4.0 45.0 1.0
CE1 B:HIS178 4.0 43.9 1.0
CG1 B:VAL44 4.1 23.8 1.0
CG B:GLU183 4.2 36.4 1.0
OE1 B:GLU34 4.3 37.2 1.0
CG B:HIS36 4.3 30.9 1.0
O B:GLY119 4.3 40.1 1.0
ND1 B:HIS36 4.3 31.1 1.0
CB B:ASP45 4.3 24.8 1.0
N B:ASP45 4.5 28.3 1.0
CB B:VAL44 4.6 27.4 1.0
CA B:ASP45 4.7 27.4 1.0
O B:HOH1017 5.0 25.5 1.0

Zinc binding site 3 out of 6 in 3a6k

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Zinc binding site 3 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The E122Q Mutant Creatininase, Mn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:30.2
occ:1.00
OD2 C:ASP45 2.1 26.6 1.0
NE2 C:HIS36 2.1 30.4 1.0
OE2 C:GLU183 2.2 36.4 1.0
OE1 C:GLU183 2.7 36.5 1.0
CD C:GLU183 2.8 37.2 1.0
CL C:CL302 2.9 48.9 1.0
CG C:ASP45 3.0 28.6 1.0
CD2 C:HIS36 3.1 29.9 1.0
CE1 C:HIS36 3.1 31.5 1.0
OD1 C:ASP45 3.2 29.8 1.0
MN C:MN300 3.6 38.1 1.0
O C:HOH1044 3.8 29.6 1.0
ND1 C:HIS178 4.0 45.0 1.0
CE1 C:HIS178 4.1 44.4 1.0
CG1 C:VAL44 4.1 29.8 1.0
OE1 C:GLU34 4.2 33.9 1.0
ND1 C:HIS36 4.2 30.0 1.0
CG C:HIS36 4.3 30.4 1.0
CG C:GLU183 4.3 36.7 1.0
CB C:ASP45 4.4 27.5 1.0
O C:GLY119 4.4 35.4 1.0
N C:ASP45 4.6 29.7 1.0
CB C:VAL44 4.6 32.4 1.0
CA C:ASP45 4.7 27.3 1.0

Zinc binding site 4 out of 6 in 3a6k

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Zinc binding site 4 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

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

b:35.9
occ:1.00
OD2 D:ASP45 2.1 33.6 1.0
OE2 D:GLU183 2.2 42.1 1.0
NE2 D:HIS36 2.2 34.7 1.0
OE1 D:GLU183 2.6 44.5 1.0
CD D:GLU183 2.7 44.9 1.0
CD2 D:HIS36 3.0 37.3 1.0
CG D:ASP45 3.0 30.5 1.0
OD1 D:ASP45 3.3 34.1 1.0
CE1 D:HIS36 3.3 35.9 1.0
CL D:CL302 3.3 55.6 1.0
MN D:MN300 3.7 44.7 1.0
ND1 D:HIS178 3.9 56.5 1.0
CE1 D:HIS178 3.9 55.9 1.0
O D:HOH1223 4.0 42.8 1.0
CG D:GLU183 4.2 45.6 1.0
CG1 D:VAL44 4.2 30.7 1.0
CG D:HIS36 4.2 37.4 1.0
OE2 D:GLU34 4.3 36.5 1.0
ND1 D:HIS36 4.3 36.1 1.0
CB D:ASP45 4.4 32.0 1.0
O D:GLY119 4.5 33.6 1.0
N D:ASP45 4.6 30.1 1.0
CB D:VAL44 4.6 31.5 1.0
CA D:ASP45 4.7 31.0 1.0
O D:HOH1066 4.9 33.2 1.0

Zinc binding site 5 out of 6 in 3a6k

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Zinc binding site 5 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The E122Q Mutant Creatininase, Mn-Zn Type within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:34.6
occ:1.00
OD1 E:ASP45 2.1 28.2 1.0
NE2 E:HIS36 2.1 27.5 1.0
OE2 E:GLU183 2.2 40.7 1.0
CD E:GLU183 2.8 39.8 1.0
OE1 E:GLU183 2.8 39.5 1.0
CL E:CL302 2.9 51.9 1.0
CG E:ASP45 3.0 31.6 1.0
CE1 E:HIS36 3.1 30.3 1.0
CD2 E:HIS36 3.1 30.4 1.0
OD2 E:ASP45 3.2 29.4 1.0
MN E:MN300 3.6 38.0 1.0
O E:HOH1110 3.9 35.9 1.0
ND1 E:HIS178 3.9 47.8 1.0
OE1 E:GLU34 4.1 33.2 1.0
CE1 E:HIS178 4.1 46.2 1.0
CG1 E:VAL44 4.1 28.6 1.0
ND1 E:HIS36 4.2 29.9 1.0
CG E:HIS36 4.3 32.1 1.0
CG E:GLU183 4.3 38.5 1.0
CB E:ASP45 4.4 29.0 1.0
N E:ASP45 4.6 30.3 1.0
CB E:VAL44 4.6 31.4 1.0
O E:GLY119 4.6 35.2 1.0
CA E:ASP45 4.7 29.5 1.0
O E:HOH1025 4.9 26.2 1.0

Zinc binding site 6 out of 6 in 3a6k

Go back to Zinc Binding Sites List in 3a6k
Zinc binding site 6 out of 6 in the The E122Q Mutant Creatininase, Mn-Zn Type


Mono view


Stereo pair view

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

b:32.4
occ:1.00
OD1 F:ASP45 2.1 30.5 1.0
OE2 F:GLU183 2.2 38.4 1.0
NE2 F:HIS36 2.2 28.5 1.0
OE1 F:GLU183 2.6 37.4 1.0
CD F:GLU183 2.7 40.2 1.0
CL F:CL302 3.0 46.2 1.0
CG F:ASP45 3.0 27.2 1.0
OD2 F:ASP45 3.1 26.1 1.0
CE1 F:HIS36 3.1 30.8 1.0
CD2 F:HIS36 3.2 29.6 1.0
MN F:MN300 3.6 39.0 1.0
O F:HOH1068 4.0 32.4 1.0
ND1 F:HIS178 4.0 36.3 1.0
CE1 F:HIS178 4.0 36.2 1.0
OE1 F:GLU34 4.1 35.9 1.0
CG1 F:VAL44 4.2 29.1 1.0
CG F:GLU183 4.2 38.1 1.0
ND1 F:HIS36 4.3 30.9 1.0
CG F:HIS36 4.3 30.7 1.0
CB F:ASP45 4.3 27.7 1.0
O F:GLY119 4.5 35.3 1.0
N F:ASP45 4.6 30.1 1.0
CB F:VAL44 4.7 31.9 1.0
CA F:ASP45 4.7 29.2 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: Sat Sep 26 05:26:27 2020
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