Atomistry » Zinc » PDB 2zxc-3ad8 » 3a6d
Atomistry »
  Zinc »
    PDB 2zxc-3ad8 »
      3a6d »

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: Wed Dec 16 04:06:21 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy