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Magnesium in PDB 1cw0: Crystal Structure Analysis of Very Short Patch Repair (Vsr) Endonuclease in Complex with A Duplex Dna

Protein crystallography data

The structure of Crystal Structure Analysis of Very Short Patch Repair (Vsr) Endonuclease in Complex with A Duplex Dna, PDB code: 1cw0 was solved by S.E.Tsutakawa, H.Jingami, K.Morikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.00 / 2.30
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 63.000, 63.000, 152.500, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 23

Other elements in 1cw0:

The structure of Crystal Structure Analysis of Very Short Patch Repair (Vsr) Endonuclease in Complex with A Duplex Dna also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure Analysis of Very Short Patch Repair (Vsr) Endonuclease in Complex with A Duplex Dna (pdb code 1cw0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure Analysis of Very Short Patch Repair (Vsr) Endonuclease in Complex with A Duplex Dna, PDB code: 1cw0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1cw0

Go back to Magnesium Binding Sites List in 1cw0
Magnesium binding site 1 out of 2 in the Crystal Structure Analysis of Very Short Patch Repair (Vsr) Endonuclease in Complex with A Duplex Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure Analysis of Very Short Patch Repair (Vsr) Endonuclease in Complex with A Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg202

b:24.9
occ:1.00
O A:HOH596 1.9 22.4 1.0
O A:HOH498 2.0 14.9 1.0
OP3 O:DT354 2.2 18.0 1.0
O3' N:DC353 2.3 26.5 1.0
O A:HOH496 2.3 21.4 1.0
OD1 A:ASP51 2.4 22.9 1.0
CG A:ASP51 3.5 21.8 1.0
O A:ARG49 3.6 18.4 1.0
C3' N:DC353 3.6 27.9 1.0
P O:DT354 3.6 20.2 1.0
MG A:MG203 3.9 22.4 1.0
NE2 A:GLN42 4.0 18.4 1.0
OP1 O:DT354 4.0 22.8 1.0
OE1 A:GLN42 4.1 20.3 1.0
O5' O:DT354 4.1 20.5 1.0
OD2 A:ASP51 4.1 20.5 1.0
O A:HOH497 4.2 30.9 1.0
C4' N:DC353 4.3 26.6 1.0
C5' O:DT354 4.3 22.4 1.0
O O:HOH472 4.4 17.7 1.0
OE2 A:GLU25 4.4 25.2 1.0
O A:HOH494 4.4 19.0 1.0
O A:GLY48 4.4 24.1 1.0
CD A:GLN42 4.5 21.8 1.0
O A:THR19 4.5 22.5 1.0
C5' N:DC353 4.5 26.3 1.0
N A:ASP51 4.6 18.1 1.0
CA A:ASP51 4.6 20.5 1.0
C2' N:DC353 4.6 25.9 1.0
CB A:ASP51 4.7 17.3 1.0
O O:HOH495 4.7 26.3 1.0
OP2 O:DT354 4.7 23.8 1.0
C A:ARG49 4.7 19.6 1.0
CG A:ARG49 4.8 27.6 1.0

Magnesium binding site 2 out of 2 in 1cw0

Go back to Magnesium Binding Sites List in 1cw0
Magnesium binding site 2 out of 2 in the Crystal Structure Analysis of Very Short Patch Repair (Vsr) Endonuclease in Complex with A Duplex Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure Analysis of Very Short Patch Repair (Vsr) Endonuclease in Complex with A Duplex Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:22.4
occ:1.00
O O:HOH495 2.1 26.3 1.0
O A:HOH494 2.1 19.0 1.0
O A:THR63 2.3 19.7 1.0
OP3 O:DT354 2.3 18.0 1.0
OP2 O:DT354 2.3 23.8 1.0
OD2 A:ASP51 2.4 20.5 1.0
P O:DT354 2.8 20.2 1.0
CG A:ASP51 3.2 21.8 1.0
OD1 A:ASP51 3.3 22.9 1.0
C A:THR63 3.4 21.0 1.0
OG1 A:THR63 3.7 20.4 1.0
N A:THR63 3.8 18.6 1.0
OP1 O:DT354 3.9 22.8 1.0
MG N:MG202 3.9 24.9 1.0
O5' O:DT354 4.0 20.5 1.0
C5' O:DT354 4.1 22.4 1.0
CA A:THR63 4.1 19.6 1.0
OE2 A:GLU25 4.2 25.2 1.0
O O:HOH472 4.2 17.7 1.0
OP1 O:DA355 4.2 21.3 1.0
O A:HOH596 4.3 22.4 1.0
NE2 A:HIS69 4.3 27.5 1.0
ND1 A:HIS64 4.3 20.7 1.0
N A:HIS64 4.4 21.0 1.0
O A:HOH496 4.4 21.4 1.0
CB A:THR63 4.5 19.3 1.0
CA A:HIS64 4.5 21.4 1.0
CB A:ASP51 4.6 17.3 1.0
C A:PHE62 4.7 18.6 1.0
OP2 O:DA355 4.9 22.4 1.0
CD2 A:PHE62 5.0 18.5 1.0
CE1 A:HIS69 5.0 25.7 1.0

Reference:

S.E.Tsutakawa, H.Jingami, K.Morikawa. Recognition of A Tg Mismatch: the Crystal Structure of Very Short Patch Repair Endonuclease in Complex with A Dna Duplex. Cell(Cambridge,Mass.) V. 99 615 1999.
ISSN: ISSN 0092-8674
PubMed: 10612397
DOI: 10.1016/S0092-8674(00)81550-0
Page generated: Mon Dec 14 05:49:06 2020

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