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Magnesium in PDB 3hne: Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp

Enzymatic activity of Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp

All present enzymatic activity of Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp, PDB code: 3hne was solved by J.W.Fairman, S.R.Wijerathna, H.Xu, C.G.Dealwis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.07 / 3.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.147, 114.372, 222.474, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 27.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp (pdb code 3hne). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp, PDB code: 3hne:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3hne

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:56.6
occ:1.00
 O2A A:TTP806 1.7 62.9 1.0
O2B A:TTP806 2.2 69.2 1.0
O3G A:TTP806 2.3 75.5 1.0
PA A:TTP806 3.1 62.3 1.0
PB A:TTP806 3.3 70.1 1.0
CB A:SER227 3.6 61.4 1.0
PG A:TTP806 3.6 75.5 1.0
O3A A:TTP806 3.7 65.1 1.0
O1A A:TTP806 3.8 60.4 1.0
O3B A:TTP806 3.9 71.9 1.0
O A:ASP226 4.2 63.0 1.0
O5' A:TTP806 4.3 62.7 1.0
CA A:SER227 4.3 60.6 1.0
C5' A:TTP806 4.4 63.6 1.0
O1G A:TTP806 4.5 74.8 1.0
NZ B:LYS243 4.5 71.5 1.0
O1B A:TTP806 4.6 71.2 1.0
O2G A:TTP806 4.7 74.3 1.0
NH1 A:ARG256 4.8 63.0 1.0
OG A:SER227 4.8 62.1 1.0

Magnesium binding site 2 out of 4 in 3hne

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:62.5
occ:1.00
 O2A B:TTP805 2.1 74.6 1.0
O2B B:TTP805 2.4 80.7 1.0
O3G B:TTP805 2.5 85.4 1.0
O1G B:TTP805 2.5 83.4 1.0
PG B:TTP805 3.0 84.0 1.0
PB B:TTP805 3.3 82.1 1.0
PA B:TTP805 3.3 74.7 1.0
O3B B:TTP805 3.5 82.7 1.0
O3A B:TTP805 3.6 79.1 1.0
O B:ASP226 4.1 63.9 1.0
O1A B:TTP805 4.2 73.8 1.0
CB B:SER227 4.2 61.5 1.0
O2G B:TTP805 4.4 82.0 1.0
O5' B:TTP805 4.5 73.2 1.0
C5' B:TTP805 4.5 72.6 1.0
NH1 B:ARG256 4.6 69.5 1.0
CA B:SER227 4.7 61.2 1.0
O1B B:TTP805 4.7 82.3 1.0

Magnesium binding site 3 out of 4 in 3hne

Go back to Magnesium Binding Sites List in 3hne
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:42.6
occ:1.00
 O3B B:ATP807 2.6 76.5 1.0
O1B B:ATP807 3.1 75.7 1.0
O2G B:ATP807 3.3 73.7 1.0
PG B:ATP807 3.3 76.0 1.0
PB B:ATP807 3.3 76.9 1.0
O3G B:ATP807 3.4 72.4 1.0
O2B B:ATP807 4.0 76.2 1.0
NZ B:LYS88 4.5 75.4 1.0
O1G B:ATP807 4.8 74.1 1.0
O3A B:ATP807 4.8 72.9 1.0

Magnesium binding site 4 out of 4 in 3hne

Go back to Magnesium Binding Sites List in 3hne
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Ribonucleotide Reductase 1 Bound to the Effectors Ttp and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg804

b:47.3
occ:1.00
 O1A B:ATP807 1.6 72.2 1.0
O2B B:ATP807 2.2 76.2 1.0
PA B:ATP807 2.9 69.7 1.0
O3A B:ATP807 3.3 72.9 1.0
PB B:ATP807 3.3 76.9 1.0
O2A B:ATP807 3.5 66.7 1.0
CB B:ARG6 3.9 71.1 1.0
O5' B:ATP807 4.1 65.9 1.0
CD B:ARG6 4.2 68.7 1.0
O1B B:ATP807 4.3 75.7 1.0
CG B:ARG6 4.3 69.6 1.0
O3B B:ATP807 4.4 76.5 1.0
NZ B:LYS5 4.7 66.5 1.0
NE B:ARG6 4.8 68.1 1.0
N B:ARG6 4.9 73.2 1.0
CA B:ARG6 4.9 72.5 1.0

Reference:

J.W.Fairman, S.R.Wijerathna, M.F.Ahmad, H.Xu, R.Nakano, S.Jha, J.Prendergast, R.M.Welin, S.Flodin, A.Roos, P.Nordlund, Z.Li, T.Walz, C.G.Dealwis. Structural Basis For Allosteric Regulation of Human Ribonucleotide Reductase By Nucleotide-Induced Oligomerization. Nat.Struct.Mol.Biol. V. 18 316 2011.
ISSN: ISSN 1545-9993
PubMed: 21336276
DOI: 10.1038/NSMB.2007
Page generated: Wed Aug 14 15:12:55 2024

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