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Zinc in PDB 3a6g: W154F Mutant Creatininase

Enzymatic activity of W154F Mutant Creatininase

All present enzymatic activity of W154F Mutant Creatininase:
3.5.2.10;

Protein crystallography data

The structure of W154F Mutant Creatininase, PDB code: 3a6g 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 (°) 164.500, 164.500, 164.100, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 21.6

Other elements in 3a6g:

The structure of W154F Mutant Creatininase also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the W154F Mutant Creatininase (pdb code 3a6g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the W154F Mutant Creatininase, PDB code: 3a6g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3a6g

Go back to Zinc Binding Sites List in 3a6g
Zinc binding site 1 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:32.1
occ:1.00
 OD1 A:ASP45 2.1 13.0 1.0
OE1 A:GLU183 2.1 21.0 1.0
O A:HOH1001 2.2 19.2 1.0
NE2 A:HIS36 2.2 13.3 1.0
CD A:GLU183 2.9 21.1 1.0
OE2 A:GLU183 2.9 19.0 1.0
CG A:ASP45 3.0 14.9 1.0
CE1 A:HIS36 3.1 14.3 1.0
CD2 A:HIS36 3.2 13.1 1.0
OD2 A:ASP45 3.2 15.1 1.0
MN A:MN300 3.6 23.7 1.0
O A:HOH1251 3.6 31.5 1.0
O A:HOH1515 3.7 41.3 1.0
ND1 A:HIS178 3.9 17.6 1.0
OE1 A:GLU34 4.2 16.4 1.0
ND1 A:HIS36 4.2 15.4 1.0
CE1 A:HIS178 4.2 17.2 1.0
CG1 A:VAL44 4.2 15.8 1.0
CG A:GLU183 4.3 18.6 1.0
CG A:HIS36 4.3 13.6 1.0
CB A:ASP45 4.3 13.5 1.0
O A:GLY119 4.5 15.9 1.0
N A:ASP45 4.6 12.7 1.0
CA A:ASP45 4.7 13.1 1.0
CB A:VAL44 4.8 15.8 1.0
O A:HOH1032 5.0 14.6 1.0

Zinc binding site 2 out of 6 in 3a6g

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Zinc binding site 2 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:30.1
occ:1.00
 OE1 B:GLU183 2.1 22.2 1.0
OD1 B:ASP45 2.1 15.4 1.0
O B:HOH1003 2.1 17.1 1.0
NE2 B:HIS36 2.2 13.2 1.0
CD B:GLU183 2.8 21.2 1.0
OE2 B:GLU183 2.8 19.9 1.0
CG B:ASP45 3.0 15.2 1.0
CE1 B:HIS36 3.2 15.1 1.0
CD2 B:HIS36 3.2 14.5 1.0
OD2 B:ASP45 3.2 15.2 1.0
MN B:MN300 3.5 23.9 1.0
O B:HOH1198 3.7 28.4 1.0
ND1 B:HIS178 3.9 17.1 1.0
O B:HOH1013 3.9 32.9 1.0
CE1 B:HIS178 4.1 17.2 1.0
OE2 B:GLU34 4.2 14.8 1.0
CG B:GLU183 4.3 20.1 1.0
ND1 B:HIS36 4.3 14.1 1.0
CG1 B:VAL44 4.3 17.9 1.0
CG B:HIS36 4.3 14.6 1.0
CB B:ASP45 4.4 14.4 1.0
O B:GLY119 4.5 15.9 1.0
N B:ASP45 4.7 13.8 1.0
CA B:ASP45 4.7 14.7 1.0
CB B:VAL44 4.8 16.7 1.0
O B:HOH1004 5.0 17.4 1.0

Zinc binding site 3 out of 6 in 3a6g

Go back to Zinc Binding Sites List in 3a6g
Zinc binding site 3 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:34.3
occ:1.00
 OD1 C:ASP45 2.1 15.3 1.0
OE1 C:GLU183 2.1 25.3 1.0
NE2 C:HIS36 2.2 15.9 1.0
O C:HOH1005 2.2 21.5 1.0
CD C:GLU183 2.8 25.0 1.0
OE2 C:GLU183 2.9 24.0 1.0
CG C:ASP45 3.1 14.7 1.0
CE1 C:HIS36 3.1 16.0 1.0
CD2 C:HIS36 3.3 15.1 1.0
OD2 C:ASP45 3.3 15.4 1.0
O C:HOH1402 3.6 36.0 1.0
MN C:MN300 3.7 24.1 1.0
O C:HOH1014 3.8 32.6 1.0
ND1 C:HIS178 3.9 19.4 1.0
CE1 C:HIS178 4.2 18.9 1.0
OE1 C:GLU34 4.2 18.8 1.0
ND1 C:HIS36 4.2 16.5 1.0
CG1 C:VAL44 4.3 16.5 1.0
CG C:GLU183 4.3 23.1 1.0
CG C:HIS36 4.3 16.0 1.0
CB C:ASP45 4.4 14.2 1.0
O C:GLY119 4.5 16.8 1.0
N C:ASP45 4.6 14.2 1.0
CB C:VAL44 4.7 16.5 1.0
CA C:ASP45 4.7 14.9 1.0

Zinc binding site 4 out of 6 in 3a6g

Go back to Zinc Binding Sites List in 3a6g
Zinc binding site 4 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:31.9
occ:1.00
 OE1 D:GLU183 2.1 27.4 1.0
OD1 D:ASP45 2.1 15.2 1.0
NE2 D:HIS36 2.2 15.0 1.0
O D:HOH1007 2.2 19.4 1.0
CD D:GLU183 2.8 25.0 1.0
OE2 D:GLU183 2.8 25.5 1.0
CG D:ASP45 3.1 15.4 1.0
CE1 D:HIS36 3.1 17.3 1.0
CD2 D:HIS36 3.2 16.7 1.0
OD2 D:ASP45 3.4 16.6 1.0
MN D:MN300 3.6 25.4 1.0
O D:HOH1339 3.8 23.1 1.0
ND1 D:HIS178 3.9 16.5 1.0
O D:HOH1015 3.9 32.7 1.0
CG D:GLU183 4.2 23.7 1.0
CE1 D:HIS178 4.2 15.7 1.0
ND1 D:HIS36 4.2 16.3 1.0
OE2 D:GLU34 4.3 16.4 1.0
CG D:HIS36 4.3 14.6 1.0
CG1 D:VAL44 4.4 16.2 1.0
O D:GLY119 4.4 17.2 1.0
CB D:ASP45 4.4 12.3 1.0
N D:ASP45 4.6 13.3 1.0
CA D:ASP45 4.7 14.2 1.0
CB D:VAL44 4.8 15.3 1.0
O D:HOH1008 5.0 16.0 1.0

Zinc binding site 5 out of 6 in 3a6g

Go back to Zinc Binding Sites List in 3a6g
Zinc binding site 5 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:30.4
occ:1.00
 OD1 E:ASP45 2.1 15.9 1.0
OE2 E:GLU183 2.1 21.2 1.0
NE2 E:HIS36 2.1 14.9 1.0
O E:HOH1009 2.2 17.4 1.0
CD E:GLU183 2.8 21.5 1.0
OE1 E:GLU183 2.9 20.6 1.0
CG E:ASP45 3.0 16.9 1.0
CE1 E:HIS36 3.1 16.1 1.0
CD2 E:HIS36 3.2 14.8 1.0
OD2 E:ASP45 3.3 17.0 1.0
MN E:MN300 3.6 22.7 1.0
O E:HOH1224 3.6 22.2 1.0
ND1 E:HIS178 3.9 18.5 1.0
O E:HOH1016 4.0 26.2 1.0
CE1 E:HIS178 4.1 16.3 1.0
ND1 E:HIS36 4.2 14.9 1.0
OE1 E:GLU34 4.2 16.8 1.0
CG E:GLU183 4.3 20.2 1.0
CG1 E:VAL44 4.3 17.4 1.0
CG E:HIS36 4.3 13.9 1.0
O E:GLY119 4.4 17.1 1.0
CB E:ASP45 4.4 15.1 1.0
N E:ASP45 4.6 14.2 1.0
CA E:ASP45 4.7 14.8 1.0
CB E:VAL44 4.7 16.6 1.0
O E:HOH1031 5.0 15.2 1.0

Zinc binding site 6 out of 6 in 3a6g

Go back to Zinc Binding Sites List in 3a6g
Zinc binding site 6 out of 6 in the W154F Mutant Creatininase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of W154F Mutant Creatininase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:30.7
occ:1.00
 OD1 F:ASP45 2.1 16.6 1.0
OE1 F:GLU183 2.1 23.2 1.0
NE2 F:HIS36 2.2 16.3 1.0
O F:HOH1011 2.2 22.7 1.0
CD F:GLU183 2.8 22.5 1.0
OE2 F:GLU183 2.9 21.7 1.0
CG F:ASP45 3.1 16.5 1.0
CE1 F:HIS36 3.1 17.0 1.0
CD2 F:HIS36 3.2 17.1 1.0
OD2 F:ASP45 3.3 18.7 1.0
O F:HOH1017 3.4 44.5 1.0
O F:HOH1134 3.6 25.5 1.0
MN F:MN300 3.7 26.7 1.0
ND1 F:HIS178 3.8 18.7 1.0
CE1 F:HIS178 4.1 18.8 1.0
OE2 F:GLU34 4.2 15.4 1.0
ND1 F:HIS36 4.3 16.0 1.0
CG1 F:VAL44 4.3 16.1 1.0
CG F:GLU183 4.3 22.2 1.0
CG F:HIS36 4.3 16.7 1.0
O F:GLY119 4.4 16.2 1.0
CB F:ASP45 4.4 15.0 1.0
N F:ASP45 4.6 14.4 1.0
CB F:VAL44 4.7 16.1 1.0
CA F:ASP45 4.7 15.2 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: Thu Oct 24 11:05:56 2024

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