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Chlorine in PDB 5kgm: 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form)

Enzymatic activity of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form)

All present enzymatic activity of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form):
5.4.2.12;

Protein crystallography data

The structure of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form), PDB code: 5kgm was solved by S.Lovell, N.Mehzabeen, K.P.Battaile, H.Yu, P.Dranchak, R.Macarthur, Z.Li, T.Carlow, H.Suga, J.Inglese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.98 / 2.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.850, 94.375, 102.201, 90.00, 96.57, 90.00
R / Rfree (%) 18.4 / 23.7

Other elements in 5kgm:

The structure of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) also contains other interesting chemical elements:

Manganese (Mn) 2 atoms
Zinc (Zn) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) (pdb code 5kgm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form), PDB code: 5kgm:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5kgm

Go back to Chlorine Binding Sites List in 5kgm
Chlorine binding site 1 out of 4 in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:34.2
occ:1.00
 N A:ASN336 3.3 44.7 1.0
NH1 A:ARG97 3.5 39.4 1.0
CA A:ASN336 3.8 35.7 1.0
N A:LYS337 4.1 39.2 1.0
N A:SER335 4.3 52.3 1.0
OD1 A:ASN336 4.3 50.6 1.0
C A:SER335 4.3 47.1 1.0
CB A:SER335 4.4 47.0 1.0
C A:ASN336 4.5 37.7 1.0
CA A:SER335 4.5 37.7 1.0
CZ A:ARG97 4.7 37.7 1.0
CD A:ARG97 4.8 26.4 1.0
CG A:GLU529 4.9 36.9 1.0

Chlorine binding site 2 out of 4 in 5kgm

Go back to Chlorine Binding Sites List in 5kgm
Chlorine binding site 2 out of 4 in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:44.9
occ:1.00
 NH2 A:ARG216 3.3 46.4 1.0
NH2 A:ARG284 3.5 58.6 1.0
NE A:ARG287 3.8 67.5 1.0
NE2 A:HIS147 3.8 49.8 1.0
NH2 A:ARG287 3.8 39.8 1.0
CZ A:ARG216 4.1 46.1 1.0
NH1 A:ARG216 4.2 56.7 1.0
CZ A:ARG287 4.3 47.0 1.0
CZ A:ARG284 4.3 52.8 1.0
CE1 A:HIS147 4.5 45.1 1.0
CZ A:ARG177 4.6 91.4 1.0
NH2 A:ARG177 4.7 84.6 1.0
NH2 A:ARG210 4.7 48.1 1.0
NE A:ARG177 4.8 74.2 1.0
NH1 A:ARG177 4.8 96.2 1.0
NH1 A:ARG284 4.9 58.7 1.0
CD2 A:HIS147 4.9 46.3 1.0
CD A:ARG287 4.9 47.4 1.0
NE A:ARG284 5.0 41.0 1.0

Chlorine binding site 3 out of 4 in 5kgm

Go back to Chlorine Binding Sites List in 5kgm
Chlorine binding site 3 out of 4 in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:37.7
occ:1.00
 N B:ASN336 3.3 56.9 1.0
NH1 B:ARG97 3.6 41.6 1.0
CA B:ASN336 3.8 36.1 1.0
N B:LYS337 3.9 43.9 1.0
CB B:SER335 4.0 48.9 1.0
N B:SER335 4.1 48.7 1.0
C B:SER335 4.2 50.6 1.0
CA B:SER335 4.3 34.9 1.0
C B:ASN336 4.4 38.2 1.0
OD1 B:ASN336 4.7 46.4 1.0
CG B:GLU529 4.8 40.7 1.0
CZ B:ARG97 4.9 42.3 1.0
CB B:LYS337 5.0 38.9 1.0
CD B:ARG97 5.0 31.6 1.0
CA B:LYS337 5.0 39.4 1.0

Chlorine binding site 4 out of 4 in 5kgm

Go back to Chlorine Binding Sites List in 5kgm
Chlorine binding site 4 out of 4 in the 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 2.95A Resolution Structure of Apo Independent Phosphoglycerate Mutase From C. Elegans (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:49.5
occ:1.00
 NH2 B:ARG216 3.6 75.7 1.0
NH2 B:ARG284 3.6 50.7 1.0
NH2 B:ARG287 3.8 63.0 1.0
NE B:ARG287 3.9 69.2 1.0
CE1 B:HIS147 4.0 55.7 1.0
NH1 B:ARG216 4.2 75.2 1.0
CZ B:ARG216 4.2 72.3 1.0
CZ B:ARG287 4.3 65.5 1.0
CZ B:ARG284 4.4 60.1 1.0
NE2 B:HIS147 4.5 48.5 1.0
NH2 B:ARG210 4.8 62.7 1.0
NH1 B:ARG284 4.8 67.4 1.0

Reference:

H.Yu, P.Dranchak, Z.Li, R.Macarthur, M.S.Munson, N.Mehzabeen, N.J.Baird, K.P.Battalie, D.Ross, S.Lovell, C.K.Carlow, H.Suga, J.Inglese. Macrocycle Peptides Delineate Locked-Open Inhibition Mechanism For Microorganism Phosphoglycerate Mutases. Nat Commun V. 8 14932 2017.
ISSN: ESSN 2041-1723
PubMed: 28368002
DOI: 10.1038/NCOMMS14932
Page generated: Sat Dec 12 11:56:28 2020

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