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Manganese in PDB 1v7z: Creatininase-Product Complex

Enzymatic activity of Creatininase-Product Complex

All present enzymatic activity of Creatininase-Product Complex:
3.5.2.10;

Protein crystallography data

The structure of Creatininase-Product Complex, PDB code: 1v7z was solved by T.Yoshimoto, N.Tanaka, N.Kanada, T.Inoue, Y.Nakajima, M.Haratake, K.T.Nakamura, Y.Xu, K.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.186, 152.211, 167.119, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 19.8

Other elements in 1v7z:

The structure of Creatininase-Product Complex also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Creatininase-Product Complex (pdb code 1v7z). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Creatininase-Product Complex, PDB code: 1v7z:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 1v7z

Go back to Manganese Binding Sites List in 1v7z
Manganese binding site 1 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Creatininase-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:18.0
occ:1.00
 OD2 A:ASP45 2.1 19.3 1.0
OE2 A:GLU34 2.1 17.1 1.0
O8 A:CRN401 2.3 21.4 1.0
ND1 A:HIS120 2.3 16.6 1.0
O A:HOH1001 2.3 23.9 1.0
O9 A:CRN401 2.4 25.0 1.0
C7 A:CRN401 2.7 27.0 1.0
CE1 A:HIS120 3.1 16.8 1.0
CD A:GLU34 3.1 15.9 1.0
CG A:ASP45 3.2 17.6 1.0
CG A:HIS120 3.3 16.7 1.0
OE1 A:GLU34 3.5 16.0 1.0
ZN A:ZN301 3.6 20.5 1.0
OD1 A:ASP45 3.6 18.0 1.0
CB A:HIS120 3.8 16.7 1.0
CA A:HIS120 3.8 16.3 1.0
N3 A:CRN401 4.1 28.5 1.0
OE1 A:GLU122 4.1 17.2 1.0
CE1 A:HIS178 4.1 21.9 1.0
ND1 A:HIS178 4.2 22.2 1.0
C5 A:CRN401 4.2 26.4 1.0
NE2 A:HIS120 4.2 17.1 1.0
N A:TYR121 4.3 17.1 1.0
NE2 A:HIS36 4.3 18.4 1.0
CD2 A:HIS120 4.4 17.5 1.0
CG A:GLU34 4.4 17.0 1.0
CE1 A:HIS36 4.4 18.5 1.0
CB A:ASP45 4.5 17.4 1.0
C A:HIS120 4.5 16.5 1.0
O A:GLY119 4.6 17.3 1.0
CB A:GLU34 4.6 16.6 1.0
CB A:ALA32 4.9 15.0 1.0
C2 A:CRN401 4.9 28.3 1.0
N1 A:CRN401 5.0 27.8 1.0

Manganese binding site 2 out of 6 in 1v7z

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Manganese binding site 2 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Creatininase-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn3300

b:18.8
occ:1.00
 OE2 B:GLU34 2.0 19.5 1.0
OD2 B:ASP45 2.1 20.3 1.0
O8 B:CRN3401 2.3 22.4 1.0
ND1 B:HIS120 2.3 17.0 1.0
O B:HOH1003 2.3 21.9 1.0
O9 B:CRN3401 2.3 28.6 1.0
C7 B:CRN3401 2.6 29.7 1.0
CE1 B:HIS120 3.1 17.2 1.0
CD B:GLU34 3.1 16.6 1.0
CG B:ASP45 3.2 18.9 1.0
CG B:HIS120 3.4 17.3 1.0
OE1 B:GLU34 3.5 17.9 1.0
ZN B:ZN3301 3.5 21.8 1.0
OD1 B:ASP45 3.7 17.5 1.0
CB B:HIS120 3.9 17.9 1.0
CA B:HIS120 3.9 17.8 1.0
ND1 B:HIS178 4.1 22.9 1.0
OE1 B:GLU122 4.1 18.4 1.0
N3 B:CRN3401 4.1 34.5 1.0
CE1 B:HIS178 4.1 23.0 1.0
C5 B:CRN3401 4.1 30.6 1.0
NE2 B:HIS120 4.3 18.1 1.0
N B:TYR121 4.3 18.4 1.0
NE2 B:HIS36 4.4 21.1 1.0
CG B:GLU34 4.4 17.8 1.0
CD2 B:HIS120 4.4 18.1 1.0
CE1 B:HIS36 4.5 20.4 1.0
CB B:ASP45 4.5 18.6 1.0
C B:HIS120 4.6 18.2 1.0
O B:GLY119 4.6 18.1 1.0
CB B:GLU34 4.6 17.7 1.0
CB B:ALA32 4.9 16.9 1.0
C2 B:CRN3401 4.9 33.4 1.0
N1 B:CRN3401 4.9 31.9 1.0

Manganese binding site 3 out of 6 in 1v7z

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Manganese binding site 3 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Creatininase-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn4300

b:19.3
occ:1.00
 OE2 C:GLU34 2.0 19.4 1.0
O C:HOH1005 2.1 22.5 1.0
OD2 C:ASP45 2.1 18.4 1.0
O8 C:CRN4401 2.3 25.5 1.0
ND1 C:HIS120 2.3 18.5 1.0
O9 C:CRN4401 2.5 32.3 1.0
C7 C:CRN4401 2.7 33.4 1.0
CD C:GLU34 3.1 18.8 1.0
CE1 C:HIS120 3.1 19.2 1.0
CG C:ASP45 3.2 18.3 1.0
CG C:HIS120 3.4 19.4 1.0
OE1 C:GLU34 3.5 19.0 1.0
ZN C:ZN4301 3.5 22.0 1.0
OD1 C:ASP45 3.7 17.1 1.0
CB C:HIS120 3.9 19.7 1.0
CA C:HIS120 3.9 19.8 1.0
ND1 C:HIS178 4.0 22.1 1.0
OE1 C:GLU122 4.1 18.8 1.0
CE1 C:HIS178 4.1 21.2 1.0
C5 C:CRN4401 4.2 35.0 1.0
NE2 C:HIS120 4.3 19.8 1.0
NE2 C:HIS36 4.3 21.8 1.0
CG C:GLU34 4.4 18.4 1.0
CD2 C:HIS120 4.4 19.6 1.0
N C:TYR121 4.5 21.0 1.0
CB C:ASP45 4.5 18.0 1.0
CE1 C:HIS36 4.5 20.5 1.0
N3 C:CRN4401 4.5 42.2 1.0
C C:HIS120 4.6 20.1 1.0
CB C:GLU34 4.6 17.9 1.0
O C:GLY119 4.7 19.9 1.0
CB C:ALA32 4.9 16.7 1.0

Manganese binding site 4 out of 6 in 1v7z

Go back to Manganese Binding Sites List in 1v7z
Manganese binding site 4 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Creatininase-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn5300

b:20.4
occ:1.00
 OE2 D:GLU34 1.9 19.2 1.0
OD2 D:ASP45 2.1 21.6 1.0
O D:HOH1007 2.2 23.8 1.0
O8 D:CRN5401 2.2 22.1 1.0
ND1 D:HIS120 2.3 19.5 1.0
O9 D:CRN5401 2.4 31.6 1.0
C7 D:CRN5401 2.7 31.9 1.0
CD D:GLU34 3.0 19.8 1.0
CE1 D:HIS120 3.0 21.7 1.0
CG D:ASP45 3.3 21.6 1.0
CG D:HIS120 3.4 20.4 1.0
OE1 D:GLU34 3.4 19.0 1.0
ZN D:ZN5301 3.5 23.4 1.0
OD1 D:ASP45 3.7 19.6 1.0
CB D:HIS120 3.9 19.7 1.0
CA D:HIS120 3.9 19.9 1.0
ND1 D:HIS178 4.0 23.8 1.0
OE1 D:GLU122 4.1 18.9 1.0
CE1 D:HIS178 4.1 22.8 1.0
C5 D:CRN5401 4.2 33.4 1.0
NE2 D:HIS120 4.2 21.6 1.0
NE2 D:HIS36 4.3 21.7 1.0
N D:TYR121 4.3 19.9 1.0
CG D:GLU34 4.3 20.4 1.0
CE1 D:HIS36 4.4 21.1 1.0
CD2 D:HIS120 4.4 21.2 1.0
N3 D:CRN5401 4.4 38.6 1.0
CB D:ASP45 4.5 20.2 1.0
C D:HIS120 4.6 19.7 1.0
O D:GLY119 4.6 19.7 1.0
CB D:GLU34 4.6 20.4 1.0
CB D:ALA32 4.9 19.0 1.0
N1 D:CRN5401 5.0 34.9 1.0
C2 D:CRN5401 5.0 36.7 1.0

Manganese binding site 5 out of 6 in 1v7z

Go back to Manganese Binding Sites List in 1v7z
Manganese binding site 5 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Creatininase-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn6300

b:19.7
occ:1.00
 OE2 E:GLU34 2.0 18.4 1.0
OD2 E:ASP45 2.1 21.6 1.0
O8 E:CRN6401 2.2 21.9 1.0
O E:HOH1009 2.2 23.5 1.0
ND1 E:HIS120 2.3 20.0 1.0
O9 E:CRN6401 2.6 30.2 1.0
C7 E:CRN6401 2.7 31.0 1.0
CD E:GLU34 3.0 18.6 1.0
CE1 E:HIS120 3.0 21.0 1.0
CG E:ASP45 3.2 20.8 1.0
CG E:HIS120 3.4 20.0 1.0
OE1 E:GLU34 3.4 19.1 1.0
ZN E:ZN6301 3.5 22.3 1.0
OD1 E:ASP45 3.7 19.2 1.0
CB E:HIS120 3.9 18.9 1.0
CA E:HIS120 3.9 18.9 1.0
OE1 E:GLU122 4.1 17.1 1.0
ND1 E:HIS178 4.1 21.7 1.0
NE2 E:HIS120 4.2 20.9 1.0
C5 E:CRN6401 4.2 31.9 1.0
CE1 E:HIS178 4.2 20.2 1.0
NE2 E:HIS36 4.3 21.5 1.0
CG E:GLU34 4.3 18.3 1.0
N E:TYR121 4.3 18.6 1.0
N3 E:CRN6401 4.4 38.5 1.0
CD2 E:HIS120 4.4 20.3 1.0
CE1 E:HIS36 4.4 20.9 1.0
CB E:ASP45 4.5 19.7 1.0
C E:HIS120 4.6 18.4 1.0
CB E:GLU34 4.6 18.4 1.0
O E:GLY119 4.7 19.1 1.0
CB E:ALA32 4.9 17.4 1.0
N1 E:CRN6401 4.9 34.1 1.0
C2 E:CRN6401 5.0 35.9 1.0

Manganese binding site 6 out of 6 in 1v7z

Go back to Manganese Binding Sites List in 1v7z
Manganese binding site 6 out of 6 in the Creatininase-Product Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Creatininase-Product Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn7300

b:18.9
occ:1.00
 OE2 F:GLU34 2.1 17.5 1.0
OD2 F:ASP45 2.1 19.1 1.0
O8 F:CRN7401 2.2 25.3 1.0
O F:HOH1011 2.3 23.6 1.0
ND1 F:HIS120 2.3 18.8 1.0
O9 F:CRN7401 2.4 31.3 1.0
C7 F:CRN7401 2.6 33.2 1.0
CE1 F:HIS120 3.1 18.4 1.0
CD F:GLU34 3.1 17.4 1.0
CG F:ASP45 3.2 18.5 1.0
CG F:HIS120 3.4 18.5 1.0
OE1 F:GLU34 3.4 18.6 1.0
ZN F:ZN7301 3.5 21.1 1.0
OD1 F:ASP45 3.6 18.7 1.0
CB F:HIS120 3.9 18.6 1.0
CA F:HIS120 3.9 18.7 1.0
OE1 F:GLU122 4.1 19.8 1.0
ND1 F:HIS178 4.1 21.6 1.0
C5 F:CRN7401 4.1 34.7 1.0
CE1 F:HIS178 4.2 21.7 1.0
N3 F:CRN7401 4.2 39.9 1.0
NE2 F:HIS120 4.2 19.3 1.0
NE2 F:HIS36 4.3 19.3 1.0
CG F:GLU34 4.4 17.8 1.0
CD2 F:HIS120 4.4 19.9 1.0
N F:TYR121 4.4 19.9 1.0
CE1 F:HIS36 4.5 19.5 1.0
CB F:ASP45 4.5 17.6 1.0
C F:HIS120 4.6 19.0 1.0
CB F:GLU34 4.7 17.3 1.0
O F:GLY119 4.7 19.6 1.0
CB F:ALA32 4.9 16.7 1.0
C2 F:CRN7401 4.9 38.7 1.0

Reference:

T.Yoshimoto, N.Tanaka, N.Kanada, T.Inoue, Y.Nakajima, M.Haratake, K.T.Nakamura, Y.Xu, K.Ito. Crystal Structures of Creatininase Reveal the Substrate Binding Site and Provide An Insight Into the Catalytic Mechanism J.Mol.Biol. V. 337 399 2004.
ISSN: ISSN 0022-2836
PubMed: 15003455
DOI: 10.1016/J.JMB.2004.01.022
Page generated: Tue Dec 15 03:56:53 2020

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