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Magnesium in PDB 5kt2: Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+

Enzymatic activity of Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+

All present enzymatic activity of Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+:
2.7.7.7;

Protein crystallography data

The structure of Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+, PDB code: 5kt2 was solved by J.Y.Choi, A.Patra, M.Yeom, Y.S.Lee, Q.Zhang, M.Egli, F.P.Guengerich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.02 / 2.49
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 97.605, 97.605, 203.000, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+ (pdb code 5kt2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+, PDB code: 5kt2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5kt2

Go back to Magnesium Binding Sites List in 5kt2
Magnesium binding site 1 out of 3 in the Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:28.5
occ:1.00
 OD2 A:ASP59 2.0 35.8 1.0
O1G A:0KX501 2.1 34.6 1.0
O2A A:0KX501 2.1 31.7 1.0
O2B A:0KX501 2.2 29.0 1.0
O A:LEU60 2.2 37.6 1.0
OD2 A:ASP151 2.3 29.6 1.0
CG A:ASP59 3.1 32.0 1.0
MG A:MG503 3.2 35.4 0.7
C A:LEU60 3.4 34.5 1.0
PG A:0KX501 3.4 33.3 1.0
PB A:0KX501 3.4 33.4 1.0
CG A:ASP151 3.4 34.6 1.0
PA A:0KX501 3.5 33.0 1.0
OD1 A:ASP59 3.6 48.4 1.0
N A:LEU60 3.7 37.4 1.0
O3B A:0KX501 3.8 36.2 1.0
O A:HOH632 3.8 37.6 1.0
OD1 A:ASP151 3.9 34.8 1.0
O3G A:0KX501 4.0 34.9 1.0
N3A A:0KX501 4.0 34.9 1.0
CA A:LEU60 4.1 34.7 1.0
C5' A:0KX501 4.1 35.4 1.0
C A:ASP59 4.1 34.2 1.0
O5' A:0KX501 4.2 35.0 1.0
CB A:ASP59 4.4 30.8 1.0
N A:ASP61 4.4 31.7 1.0
N A:CYS62 4.6 34.8 1.0
O2G A:0KX501 4.6 37.9 1.0
O A:ASP59 4.6 38.8 1.0
CA A:ASP59 4.6 38.3 1.0
CB A:ASP151 4.6 36.4 1.0
CB A:LEU60 4.6 34.0 1.0
O1A A:0KX501 4.7 31.9 1.0
CA A:ASP61 4.7 39.4 1.0
O1B A:0KX501 4.7 39.8 1.0
C A:ASP61 4.8 37.2 1.0
N A:PHE63 4.8 36.6 1.0

Magnesium binding site 2 out of 3 in 5kt2

Go back to Magnesium Binding Sites List in 5kt2
Magnesium binding site 2 out of 3 in the Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:35.4
occ:0.67
 O2A A:0KX501 2.2 31.7 1.0
O3' P:DC873 2.2 35.5 1.0
OE2 A:GLU152 2.5 36.2 1.0
OD1 A:ASP151 2.6 34.8 1.0
OD1 A:ASP59 2.8 48.4 1.0
OD2 A:ASP59 3.0 35.8 1.0
CG A:ASP59 3.1 32.0 1.0
PA A:0KX501 3.2 33.0 1.0
OD2 A:ASP151 3.2 29.6 1.0
MG A:MG502 3.2 28.5 1.0
CG A:ASP151 3.3 34.6 1.0
CD A:GLU152 3.3 38.4 1.0
CG A:GLU152 3.4 33.0 1.0
O1A A:0KX501 3.5 31.9 1.0
C3' P:DC873 3.6 38.6 1.0
O5' A:0KX501 3.6 35.0 1.0
O A:HOH632 3.8 37.6 1.0
O A:HOH609 4.0 31.0 1.0
C4' P:DC873 4.1 38.7 1.0
C5' A:0KX501 4.1 35.4 1.0
O1G A:0KX501 4.3 34.6 1.0
C2' P:DC873 4.3 39.2 1.0
CB A:ASP59 4.4 30.8 1.0
OE1 A:GLU152 4.5 37.5 1.0
O2B A:0KX501 4.6 29.0 1.0
C5' P:DC873 4.6 38.8 1.0
CB A:ASP151 4.8 36.4 1.0
N3A A:0KX501 4.8 34.9 1.0
CB A:GLU152 4.8 26.2 1.0
O A:ASP151 4.9 35.2 1.0
C A:ASP151 4.9 34.9 1.0

Magnesium binding site 3 out of 3 in 5kt2

Go back to Magnesium Binding Sites List in 5kt2
Magnesium binding site 3 out of 3 in the Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Teranry Complex of Human Dna Polymerase Iota(26-445) Inserting Dcmpnpp Opposite Template G in the Presence of MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:46.3
occ:1.00
 O A:LYS262 2.4 55.0 1.0
O A:ILE267 2.5 50.3 1.0
OP1 P:DC872 2.5 42.7 1.0
O A:ILE264 2.7 39.3 1.0
NZ A:LYS262 3.1 56.0 1.0
C A:ILE267 3.4 46.9 1.0
C A:LYS262 3.4 50.7 1.0
C A:ILE264 3.5 45.3 1.0
P P:DC872 3.7 40.0 1.0
N A:ILE267 3.9 45.4 1.0
OP2 P:DC872 4.0 41.0 1.0
CA A:LYS262 4.1 52.3 1.0
CA A:PRO265 4.1 45.9 1.0
N A:ILE264 4.1 34.4 1.0
N A:PRO265 4.1 46.2 1.0
CG A:LYS262 4.2 57.2 1.0
CA A:ILE267 4.2 47.5 1.0
N A:GLY266 4.3 36.8 1.0
CE A:LYS262 4.3 62.0 1.0
N A:GLY268 4.3 53.5 1.0
C A:GLU263 4.3 41.1 1.0
CD A:LYS262 4.4 64.5 1.0
N A:GLU263 4.5 48.9 1.0
CA A:ILE264 4.5 42.3 1.0
CA A:GLY268 4.5 50.0 1.0
CB A:ILE267 4.6 53.0 1.0
CA A:GLU263 4.6 48.8 1.0
C A:PRO265 4.7 41.1 1.0
CB A:LYS262 4.7 57.1 1.0
O3' P:DC871 4.7 45.5 1.0
O5' P:DC872 4.8 41.4 1.0
O A:ILE261 4.8 52.0 1.0
O A:GLU263 4.8 39.8 1.0
C A:GLY266 4.9 49.8 1.0

Reference:

J.Y.Choi, A.Patra, M.Yeom, Y.S.Lee, Q.Zhang, M.Egli, F.P.Guengerich. Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human Dna Polymerase Iota. J.Biol.Chem. V. 291 21063 2016.
ISSN: ESSN 1083-351X
PubMed: 27555320
DOI: 10.1074/JBC.M116.748285
Page generated: Sun Sep 29 19:12:26 2024

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