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Zinc in PDB 3a6d: Creatininase Complexed with 1-Methylguanidine

Enzymatic activity of Creatininase Complexed with 1-Methylguanidine

All present enzymatic activity of Creatininase Complexed with 1-Methylguanidine:
3.5.2.10;

Protein crystallography data

The structure of Creatininase Complexed with 1-Methylguanidine, PDB code: 3a6d 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 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.400, 152.700, 167.500, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 20.7

Other elements in 3a6d:

The structure of Creatininase Complexed with 1-Methylguanidine also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Creatininase Complexed with 1-Methylguanidine (pdb code 3a6d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Creatininase Complexed with 1-Methylguanidine, PDB code: 3a6d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3a6d

Go back to Zinc Binding Sites List in 3a6d
Zinc binding site 1 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

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

b:26.5
occ:1.00
 OE1 A:GLU183 2.1 27.1 1.0
OD1 A:ASP45 2.1 22.0 1.0
O A:HOH2087 2.1 22.3 1.0
NE2 A:HIS36 2.2 24.5 1.0
CD A:GLU183 2.8 23.8 1.0
OE2 A:GLU183 2.8 24.3 1.0
CG A:ASP45 3.0 21.5 1.0
CE1 A:HIS36 3.1 23.8 1.0
OD2 A:ASP45 3.2 20.3 1.0
CD2 A:HIS36 3.2 23.5 1.0
MN A:MN300 3.5 23.9 1.0
O A:HOH1205 3.5 29.7 1.0
ND1 A:HIS178 3.8 24.9 1.0
O A:HOH1276 4.0 26.3 1.0
CE1 A:HIS178 4.1 23.8 1.0
CG1 A:VAL44 4.2 25.8 1.0
OE2 A:GLU34 4.2 23.1 1.0
ND1 A:HIS36 4.2 22.7 1.0
CG A:GLU183 4.3 25.1 1.0
CG A:HIS36 4.3 24.5 1.0
CB A:ASP45 4.4 21.4 1.0
N A:ASP45 4.6 22.4 1.0
O A:GLY119 4.6 22.3 1.0
CB A:VAL44 4.6 24.2 1.0
CA A:ASP45 4.7 21.5 1.0
NH2 A:MGX302 4.8 35.5 1.0
O A:HOH1030 4.9 20.7 1.0
O A:HOH2083 5.0 24.2 1.0

Zinc binding site 2 out of 6 in 3a6d

Go back to Zinc Binding Sites List in 3a6d
Zinc binding site 2 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:26.7
occ:1.00
 O B:HOH2088 2.0 21.9 1.0
OE1 B:GLU183 2.1 23.5 1.0
OD1 B:ASP45 2.1 21.9 1.0
NE2 B:HIS36 2.2 24.7 1.0
CD B:GLU183 2.7 25.4 1.0
OE2 B:GLU183 2.8 22.5 1.0
CG B:ASP45 3.0 21.3 1.0
CD2 B:HIS36 3.1 25.6 1.0
CE1 B:HIS36 3.2 25.4 1.0
OD2 B:ASP45 3.2 22.1 1.0
MN B:MN300 3.5 23.6 1.0
O B:HOH1167 3.7 28.3 1.0
ND1 B:HIS178 3.8 23.8 1.0
O B:HOH1159 4.0 25.6 1.0
CE1 B:HIS178 4.1 22.7 1.0
CG1 B:VAL44 4.1 23.1 1.0
CG B:GLU183 4.2 24.1 1.0
OE2 B:GLU34 4.2 22.6 1.0
ND1 B:HIS36 4.3 24.4 1.0
CG B:HIS36 4.3 24.4 1.0
CB B:ASP45 4.4 20.4 1.0
O B:GLY119 4.5 22.1 1.0
N B:ASP45 4.5 21.3 1.0
CB B:VAL44 4.6 23.4 1.0
CA B:ASP45 4.7 21.3 1.0
NH2 B:MGX303 4.8 36.8 1.0
O B:HOH2084 4.9 22.7 1.0
O B:HOH1014 5.0 20.7 1.0

Zinc binding site 3 out of 6 in 3a6d

Go back to Zinc Binding Sites List in 3a6d
Zinc binding site 3 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:27.6
occ:1.00
 OD1 C:ASP45 2.1 22.6 1.0
O C:HOH1324 2.1 21.1 1.0
NE2 C:HIS36 2.1 21.6 1.0
OE1 C:GLU183 2.2 25.1 1.0
OE2 C:GLU183 2.8 23.6 1.0
CD C:GLU183 2.8 24.9 1.0
CG C:ASP45 3.0 24.2 1.0
CE1 C:HIS36 3.0 22.7 1.0
CD2 C:HIS36 3.2 22.7 1.0
OD2 C:ASP45 3.2 22.5 1.0
MN C:MN300 3.5 24.9 1.0
O C:HOH1242 3.7 37.4 1.0
ND1 C:HIS178 3.9 24.4 1.0
O C:HOH1191 3.9 28.7 1.0
CE1 C:HIS178 4.1 24.7 1.0
ND1 C:HIS36 4.2 23.2 1.0
OE2 C:GLU34 4.2 22.9 1.0
CG C:HIS36 4.3 23.6 1.0
CG C:GLU183 4.3 22.4 1.0
CG1 C:VAL44 4.3 21.4 1.0
CB C:ASP45 4.4 21.9 1.0
O C:GLY119 4.5 21.6 1.0
N C:ASP45 4.6 22.1 1.0
CB C:VAL44 4.6 22.2 1.0
CA C:ASP45 4.7 21.4 1.0
NH2 C:MGX304 4.8 45.3 1.0
O C:HOH1013 4.9 22.0 1.0

Zinc binding site 4 out of 6 in 3a6d

Go back to Zinc Binding Sites List in 3a6d
Zinc binding site 4 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:29.5
occ:1.00
 OE1 D:GLU183 2.1 30.0 1.0
OD1 D:ASP45 2.1 25.2 1.0
NE2 D:HIS36 2.1 25.7 1.0
O D:HOH1657 2.2 23.0 1.0
CD D:GLU183 2.8 28.1 1.0
OE2 D:GLU183 2.8 27.4 1.0
CG D:ASP45 3.0 26.4 1.0
CE1 D:HIS36 3.1 27.5 1.0
CD2 D:HIS36 3.1 27.9 1.0
OD2 D:ASP45 3.3 23.3 1.0
MN D:MN300 3.4 28.1 1.0
O D:HOH1129 3.7 30.5 1.0
ND1 D:HIS178 3.9 28.1 1.0
O D:HOH1209 4.0 31.1 1.0
ND1 D:HIS36 4.2 25.8 1.0
CE1 D:HIS178 4.2 25.1 1.0
CG D:GLU183 4.2 29.4 1.0
CG1 D:VAL44 4.2 25.1 1.0
OE2 D:GLU34 4.3 24.7 1.0
CG D:HIS36 4.3 27.2 1.0
CB D:ASP45 4.4 23.5 1.0
O D:GLY119 4.5 25.5 1.0
NH2 D:MGX305 4.6 49.5 1.0
N D:ASP45 4.6 24.2 1.0
CB D:VAL44 4.6 25.8 1.0
NE D:MGX305 4.7 49.1 1.0
CA D:ASP45 4.7 24.0 1.0
O D:HOH1028 5.0 24.0 1.0
O D:HOH1015 5.0 25.1 1.0

Zinc binding site 5 out of 6 in 3a6d

Go back to Zinc Binding Sites List in 3a6d
Zinc binding site 5 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:27.6
occ:1.00
 O E:HOH1326 2.1 22.7 1.0
OE1 E:GLU183 2.1 27.4 1.0
OD1 E:ASP45 2.1 24.2 1.0
NE2 E:HIS36 2.1 24.6 1.0
OE2 E:GLU183 2.7 24.2 1.0
CD E:GLU183 2.7 26.2 1.0
CG E:ASP45 3.0 24.5 1.0
CD2 E:HIS36 3.1 25.5 1.0
CE1 E:HIS36 3.1 22.6 1.0
OD2 E:ASP45 3.2 22.0 1.0
MN E:MN300 3.4 26.8 1.0
O E:HOH1477 3.7 40.0 1.0
ND1 E:HIS178 3.8 24.1 1.0
O E:HOH1124 3.9 26.5 1.0
CE1 E:HIS178 4.1 21.7 1.0
OE2 E:GLU34 4.2 22.8 1.0
CG E:GLU183 4.2 26.8 1.0
CG1 E:VAL44 4.2 23.5 1.0
ND1 E:HIS36 4.2 24.0 1.0
CG E:HIS36 4.3 23.3 1.0
CB E:ASP45 4.4 22.0 1.0
NH2 E:MGX306 4.5 49.3 1.0
O E:GLY119 4.6 21.7 1.0
N E:ASP45 4.6 23.1 1.0
CB E:VAL44 4.7 22.8 1.0
CA E:ASP45 4.7 22.6 1.0
NE E:MGX306 4.9 46.4 1.0
CG E:HIS178 5.0 24.4 1.0

Zinc binding site 6 out of 6 in 3a6d

Go back to Zinc Binding Sites List in 3a6d
Zinc binding site 6 out of 6 in the Creatininase Complexed with 1-Methylguanidine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Creatininase Complexed with 1-Methylguanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:27.0
occ:1.00
 OE1 F:GLU183 2.1 23.1 1.0
OD1 F:ASP45 2.1 20.9 1.0
O F:HOH2089 2.1 22.2 1.0
NE2 F:HIS36 2.2 20.7 1.0
CD F:GLU183 2.8 23.9 1.0
OE2 F:GLU183 2.9 23.8 1.0
CG F:ASP45 3.0 22.3 1.0
CE1 F:HIS36 3.1 21.0 1.0
CD2 F:HIS36 3.2 22.4 1.0
OD2 F:ASP45 3.3 20.6 1.0
MN F:MN300 3.5 24.6 1.0
ND1 F:HIS178 3.8 23.6 1.0
O F:HOH1469 3.8 39.2 1.0
O F:HOH1224 3.9 27.3 1.0
CE1 F:HIS178 4.1 23.4 1.0
CG1 F:VAL44 4.2 23.5 1.0
OE2 F:GLU34 4.2 23.1 1.0
ND1 F:HIS36 4.2 23.8 1.0
CG F:GLU183 4.2 23.9 1.0
CG F:HIS36 4.3 23.5 1.0
CB F:ASP45 4.4 20.4 1.0
O F:GLY119 4.5 23.4 1.0
N F:ASP45 4.5 21.3 1.0
CB F:VAL44 4.6 23.3 1.0
CA F:ASP45 4.7 21.6 1.0
NH2 F:MGX307 4.8 43.3 1.0
O F:HOH1072 4.9 22.4 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 11:03:51 2024

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