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Manganese in PDB 4ima: The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp

Enzymatic activity of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp

All present enzymatic activity of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp:
2.7.1.40;

Protein crystallography data

The structure of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp, PDB code: 4ima was solved by B.Zhang, T.Holyoak, A.W.Fenton, Q.L.Tang, C.B.Prasannan, J.P.Deng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.89 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.751, 204.727, 86.532, 90.00, 96.75, 90.00
R / Rfree (%) 19.8 / 23.3

Manganese Binding Sites:

The binding sites of Manganese atom in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp (pdb code 4ima). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp, PDB code: 4ima:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4ima

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Manganese binding site 1 out of 4 in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:37.9
occ:1.00
OE1 A:GLU284 2.1 32.9 1.0
OD2 A:ASP308 2.1 34.5 1.0
OB1 A:FLC602 2.2 33.8 1.0
OHB A:FLC602 2.2 32.9 0.8
O A:HOH894 2.3 37.0 1.0
O A:HOH886 2.3 37.8 1.0
CBC A:FLC602 2.9 32.8 1.0
CB A:FLC602 3.0 37.1 1.0
CG A:ASP308 3.2 35.8 1.0
CD A:GLU284 3.2 33.8 1.0
CB A:ASP308 3.5 33.9 1.0
OE2 A:GLU284 3.5 34.3 1.0
CG A:FLC602 3.8 35.8 0.9
OG1 A:FLC602 4.0 37.3 0.8
OB2 A:FLC602 4.1 29.2 1.0
NZ A:LYS282 4.2 31.5 1.0
CA A:FLC602 4.3 30.8 0.9
OD1 A:ASP308 4.3 39.2 1.0
CE1 A:PHE256 4.3 40.5 1.0
N A:ASP308 4.4 28.5 1.0
CGC A:FLC602 4.4 36.0 0.0
O A:HOH872 4.4 44.9 1.0
CG A:GLU284 4.5 35.9 1.0
CE A:LYS282 4.5 33.6 1.0
CA A:ASP308 4.6 30.5 1.0
CB A:ALA305 4.7 32.3 1.0
CB A:GLU284 4.8 30.7 1.0
CZ A:PHE256 4.9 41.6 1.0
CD1 A:PHE256 5.0 36.4 1.0

Manganese binding site 2 out of 4 in 4ima

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Manganese binding site 2 out of 4 in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:34.4
occ:1.00
OD2 B:ASP308 2.1 32.0 1.0
OE2 B:GLU284 2.1 30.0 1.0
OHB B:FLC602 2.2 29.5 1.0
OB2 B:FLC602 2.2 33.1 1.0
O B:HOH893 2.3 30.6 1.0
O B:HOH898 2.3 34.9 1.0
CBC B:FLC602 3.0 32.2 1.0
CB B:FLC602 3.1 33.1 0.5
CG B:ASP308 3.1 35.0 1.0
CD B:GLU284 3.1 32.2 1.0
OE1 B:GLU284 3.5 31.6 1.0
CB B:ASP308 3.6 28.7 1.0
CG B:FLC602 3.9 36.4 0.7
OG2 B:FLC602 4.0 35.1 0.6
OB1 B:FLC602 4.2 35.5 1.0
OD1 B:ASP308 4.2 36.3 1.0
NZ B:LYS282 4.2 31.6 1.0
O B:HOH895 4.3 39.2 1.0
CA B:FLC602 4.3 32.7 1.0
N B:ASP308 4.3 30.0 1.0
CGC B:FLC602 4.4 35.1 0.1
CE1 B:PHE256 4.4 35.1 1.0
CG B:GLU284 4.4 25.6 1.0
CE B:LYS282 4.5 31.4 1.0
CA B:ASP308 4.6 33.4 1.0
CB B:ALA305 4.6 30.3 1.0
CB B:GLU284 4.8 31.9 1.0
O B:HOH852 4.8 49.9 1.0
CD1 B:PHE256 5.0 36.6 1.0

Manganese binding site 3 out of 4 in 4ima

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Manganese binding site 3 out of 4 in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:36.4
occ:1.00
OHB C:FLC602 2.1 32.8 1.0
OD2 C:ASP308 2.1 33.9 1.0
OB1 C:FLC602 2.1 33.5 1.0
OE2 C:GLU284 2.1 33.1 1.0
O C:HOH759 2.3 33.3 1.0
O C:HOH906 2.3 35.7 1.0
CBC C:FLC602 2.9 31.4 1.0
CB C:FLC602 2.9 36.8 1.0
CD C:GLU284 3.1 29.8 1.0
CG C:ASP308 3.2 30.8 1.0
OE1 C:GLU284 3.6 31.7 1.0
CB C:ASP308 3.6 30.7 1.0
CG C:FLC602 3.6 35.4 1.0
OG2 C:FLC602 3.9 37.8 0.6
OB2 C:FLC602 4.1 33.1 1.0
CA C:FLC602 4.2 33.1 1.0
CGC C:FLC602 4.2 36.6 0.2
NZ C:LYS282 4.2 33.9 1.0
OD1 C:ASP308 4.3 36.9 1.0
N C:ASP308 4.3 33.1 1.0
CG C:GLU284 4.4 29.5 1.0
CE C:LYS282 4.5 28.3 1.0
CA C:ASP308 4.6 32.6 1.0
CE1 C:PHE256 4.7 38.6 1.0
CB C:ALA305 4.7 27.8 1.0
O C:HOH765 4.9 49.5 1.0
CB C:GLU284 4.9 30.8 1.0
CAC C:FLC602 4.9 35.1 0.7

Manganese binding site 4 out of 4 in 4ima

Go back to Manganese Binding Sites List in 4ima
Manganese binding site 4 out of 4 in the The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of C436M-Hlpyk in Complex with Citrate/Mn/Atp/Fru-1,6-Bp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:43.8
occ:1.00
OD2 D:ASP308 2.1 44.5 1.0
OE2 D:GLU284 2.1 33.2 1.0
OB1 D:FLC602 2.2 35.2 1.0
OHB D:FLC602 2.2 39.5 1.0
O D:HOH880 2.3 42.4 1.0
O D:HOH884 2.3 47.2 1.0
CBC D:FLC602 2.9 38.1 1.0
CB D:FLC602 3.0 42.7 1.0
CG D:ASP308 3.2 37.2 1.0
CD D:GLU284 3.2 37.6 1.0
OE1 D:GLU284 3.6 40.4 1.0
CB D:ASP308 3.6 35.6 1.0
CG D:FLC602 3.8 44.8 1.0
OG2 D:FLC602 4.0 44.0 1.0
OB2 D:FLC602 4.1 33.8 1.0
NZ D:LYS282 4.2 35.5 1.0
OD1 D:ASP308 4.2 40.4 1.0
CA D:FLC602 4.3 34.7 1.0
CGC D:FLC602 4.3 42.0 0.0
N D:ASP308 4.4 31.0 1.0
CG D:GLU284 4.4 36.8 1.0
CE D:LYS282 4.5 33.5 1.0
CE1 D:PHE256 4.5 46.0 1.0
CA D:ASP308 4.6 39.3 1.0
CB D:ALA305 4.6 27.6 1.0
CB D:GLU284 4.9 32.7 1.0
CAC D:FLC602 5.0 38.2 0.3
CD1 D:PHE256 5.0 39.3 1.0

Reference:

T.Holyoak, B.Zhang, J.Deng, Q.Tang, C.B.Prasannan, A.W.Fenton. Energetic Coupling Between An Oxidizable Cysteine and the Phosphorylatable N-Terminus of Human Liver Pyruvate Kinase. Biochemistry V. 52 466 2013.
ISSN: ISSN 0006-2960
PubMed: 23270483
DOI: 10.1021/BI301341R
Page generated: Tue Dec 15 04:22:36 2020

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