Manganese in PDB 7l3m: Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid

Enzymatic activity of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid

All present enzymatic activity of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid:
4.1.1.32;

Protein crystallography data

The structure of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid, PDB code: 7l3m was solved by J.A.Clinger, D.W.Moreau, M.J.Mcleod, T.Holyoak, R.E.Thorne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.33 / 2.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.389, 118.935, 60.3, 90, 109.42, 90
R / Rfree (%) 17.2 / 18.6

Other elements in 7l3m:

The structure of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid (pdb code 7l3m). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid, PDB code: 7l3m:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 7l3m

Go back to Manganese Binding Sites List in 7l3m
Manganese binding site 1 out of 3 in the Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:14.8
occ:1.00
O1 A:PEP703 1.6 33.7 1.0
OD1 A:ASP311 2.1 10.6 1.0
NZ A:LYS244 2.3 16.2 1.0
NE2 A:HIS264 2.4 11.6 1.0
O1P A:PEP703 2.4 30.0 1.0
O A:HOH805 2.5 21.0 1.0
C1 A:PEP703 2.6 42.6 1.0
CG A:ASP311 2.9 12.9 1.0
OD2 A:ASP311 3.0 16.2 1.0
O2 A:PEP703 3.1 54.7 1.0
C2 A:PEP703 3.2 50.9 1.0
P A:PEP703 3.3 58.4 1.0
CE1 A:HIS264 3.3 11.2 1.0
CE A:LYS244 3.3 21.7 1.0
CD2 A:HIS264 3.3 12.8 1.0
O2' A:PEP703 3.7 51.8 1.0
O3P A:PEP703 4.0 43.0 1.0
NZ A:LYS290 4.1 19.2 1.0
O A:HOH836 4.2 22.0 1.0
O A:HOH1032 4.2 24.2 1.0
CE A:LYS290 4.2 16.1 1.0
CB A:ASP311 4.3 10.9 1.0
ND1 A:HIS264 4.4 16.3 1.0
C3 A:PEP703 4.4 43.3 1.0
CG A:HIS264 4.4 9.8 1.0
O2P A:PEP703 4.5 54.0 1.0
CD A:LYS244 4.6 16.4 1.0
O A:HOH803 4.8 37.5 1.0
CA A:ASP311 5.0 12.2 1.0

Manganese binding site 2 out of 3 in 7l3m

Go back to Manganese Binding Sites List in 7l3m
Manganese binding site 2 out of 3 in the Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn706

b:33.7
occ:1.00
O A:HOH987 2.2 28.1 1.0
O1B A:GDP704 2.3 26.5 1.0
O A:HOH819 2.3 27.4 1.0
O A:HOH836 2.3 22.0 1.0
O3P A:PEP703 2.4 43.0 1.0
OG1 A:THR291 2.5 17.1 1.0
PB A:GDP704 3.4 25.2 1.0
P A:PEP703 3.5 58.4 1.0
CB A:THR291 3.6 22.0 1.0
O2B A:GDP704 3.6 40.8 1.0
O1P A:PEP703 3.7 30.0 1.0
OD2 A:ASP310 3.9 28.4 1.0
O A:HOH1032 4.0 24.2 1.0
O2P A:PEP703 4.1 54.0 1.0
N A:THR291 4.2 18.9 1.0
O1A A:GDP704 4.3 32.9 1.0
O3B A:GDP704 4.3 28.6 1.0
O A:ASP310 4.4 16.8 1.0
CA A:THR291 4.5 21.0 1.0
O A:HOH1036 4.5 22.9 1.0
CA A:GLY334 4.5 18.5 1.0
O3A A:GDP704 4.6 34.0 1.0
CG2 A:THR291 4.6 22.0 1.0
CG A:ASP310 4.6 18.4 1.0
PA A:GDP704 4.8 37.9 1.0
OD1 A:ASP311 4.8 10.6 1.0
O2 A:PEP703 4.8 54.7 1.0
N A:VAL335 4.8 16.1 1.0
CB A:LYS290 4.9 11.4 1.0
O A:PHE333 4.9 19.9 1.0
NZ A:LYS290 4.9 19.2 1.0
O2A A:GDP704 4.9 29.7 1.0
O A:HOH805 5.0 21.0 1.0

Manganese binding site 3 out of 3 in 7l3m

Go back to Manganese Binding Sites List in 7l3m
Manganese binding site 3 out of 3 in the Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pepck Mmqx Structure 40MS Post-Mixing with Oxaloacetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn707

b:79.3
occ:1.00
NE2 A:HIS502 2.4 54.7 1.0
CE1 A:HIS502 2.5 48.1 1.0
OE1 A:GLU607 2.5 41.5 1.0
OE2 A:GLU607 2.8 55.1 1.0
CD A:GLU607 2.8 42.2 1.0
O A:HOH870 2.9 25.1 1.0
O A:HOH1072 3.4 44.2 1.0
O A:HOH862 3.5 39.0 1.0
CD2 A:HIS502 3.7 45.6 1.0
ND1 A:HIS502 3.8 49.5 1.0
CG A:GLU607 4.2 31.4 1.0
CG A:HIS502 4.4 44.7 1.0
NE2 A:GLN451 4.5 20.1 1.0
O A:LEU498 4.8 17.6 1.0

Reference:

J.A.Clinger, D.W.Moreau, M.J.Mcleod, T.Holyoak, R.E.Thorne. Millisecond Mix-and-Quench Crystallography (Mmqx) Enables Time-Resolved Studies of Pepck with Remote Data Collection. Iucrj V. 8 784 2021.
ISSN: ESSN 2052-2525
PubMed: 34584739
DOI: 10.1107/S2052252521007053
Page generated: Fri Nov 5 15:43:28 2021

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy