Magnesium in PDB 3gqc: Structure of Human REV1-Dna-Dntp Ternary Complex

The structure of Structure of Human REV1-Dna-Dntp Ternary Complex, PDB code: 3gqc was solved by M.K.Swan, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.07 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.436, 172.780, 129.192, 90.00, 90.65, 90.00
R / Rfree (%)	21.4 / 26.7

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>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Structure of Human REV1-Dna-Dntp Ternary Complex (pdb code 3gqc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Structure of Human REV1-Dna-Dntp Ternary Complex, PDB code: 3gqc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:20.9 occ:1.00 O1A A:DCP101 2.2 25.4 1.0 O2B A:DCP101 2.2 22.6 1.0 O A:MET424 2.3 37.0 1.0 OD1 A:ASP423 2.3 40.1 1.0 O3G A:DCP101 2.4 21.4 1.0 OD2 A:ASP570 2.5 41.6 1.0 CG A:ASP423 3.3 39.6 1.0 PB A:DCP101 3.3 23.6 1.0 C A:MET424 3.4 36.5 1.0 PA A:DCP101 3.5 25.4 1.0 PG A:DCP101 3.5 25.1 1.0 O3A A:DCP101 3.6 23.9 1.0 CG A:ASP570 3.7 42.0 1.0 MG A:MG202 3.7 33.0 0.5 OD2 A:ASP423 3.7 43.4 1.0 O A:HOH89 3.8 47.4 1.0 O3B A:DCP101 3.8 21.4 1.0 N A:MET424 3.9 36.5 1.0 NZ A:LYS625 3.9 41.7 1.0 O2G A:DCP101 3.9 25.8 1.0 C5' A:DCP101 4.2 25.3 1.0 CA A:MET424 4.2 36.5 1.0 OD1 A:ASP570 4.3 44.2 1.0 O5' A:DCP101 4.3 25.6 1.0 C A:ASP423 4.4 36.7 1.0 N A:ASP425 4.5 36.3 1.0 CE A:LYS625 4.6 42.8 1.0 CB A:ASP423 4.6 36.9 1.0 N A:CYS426 4.6 35.5 1.0 O2A A:DCP101 4.7 25.7 1.0 CA A:ASP425 4.7 36.1 1.0 CB A:MET424 4.7 36.5 1.0 O1B A:DCP101 4.7 25.2 1.0 CB A:PHE427 4.7 32.8 1.0 OE1 A:GLU571 4.8 52.1 1.0 CB A:ASP570 4.8 41.3 1.0 O1G A:DCP101 4.8 23.8 1.0 CA A:ASP423 4.8 36.6 1.0 C A:ASP425 4.8 35.9 1.0 N A:PHE427 4.8 34.0 1.0 O A:ASP570 4.9 41.5 1.0 O A:ASP423 4.9 37.3 1.0

Magnesium binding site 2 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:33.0 occ:0.50 O1A A:DCP101 2.3 25.4 1.0 OD1 A:ASP570 2.4 44.2 1.0 OE1 A:GLU571 2.7 52.1 1.0 OD2 A:ASP570 3.1 41.6 1.0 CG A:ASP570 3.1 42.0 1.0 PA A:DCP101 3.1 25.4 1.0 C3' E:DOC12 3.3 32.6 1.0 OG A:SER568 3.3 44.0 1.0 C5' A:DCP101 3.4 25.3 1.0 O5' A:DCP101 3.4 25.6 1.0 O2A A:DCP101 3.7 25.7 1.0 MG A:MG201 3.7 20.9 1.0 C2' E:DOC12 3.8 32.1 1.0 OD1 A:ASP423 3.9 40.1 1.0 CD A:GLU571 3.9 50.1 1.0 CB A:GLU571 4.1 41.2 1.0 O A:HOH89 4.1 47.4 1.0 C4' E:DOC12 4.2 33.3 1.0 CB A:SER568 4.4 42.8 1.0 CG A:GLU571 4.5 44.1 1.0 CB A:ASP570 4.6 41.3 1.0 O3A A:DCP101 4.6 23.9 1.0 CG A:ASP423 4.6 39.6 1.0 O2B A:DCP101 4.7 22.6 1.0 OD2 A:ASP423 4.8 43.4 1.0 C4' A:DCP101 4.8 26.7 1.0 C A:ASP570 4.8 41.3 1.0 O5' E:DOC12 4.9 39.5 1.0 OE2 A:GLU571 4.9 51.7 1.0 O A:ASP570 5.0 41.5 1.0 N A:ASP570 5.0 42.2 1.0

Magnesium binding site 3 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg209 b:40.6 occ:1.00 O A:GLU507 2.6 35.3 1.0 OP2 F:DA3 2.8 38.7 1.0 OH A:TYR541 2.8 33.0 1.0 N A:SER448 2.9 37.1 1.0 OG A:SER448 3.3 36.5 1.0 OG1 A:THR447 3.4 37.5 1.0 CA A:THR447 3.4 36.5 1.0 C A:THR447 3.6 36.8 1.0 CE1 A:TYR541 3.6 36.4 1.0 CZ A:TYR541 3.6 36.0 1.0 C A:GLU507 3.7 35.7 1.0 CB A:SER448 3.8 37.9 1.0 N A:GLU507 3.8 36.0 1.0 CB A:THR447 3.9 36.5 1.0 CA A:SER448 3.9 37.8 1.0 P F:DA3 4.0 39.2 1.0 CB A:ALA506 4.2 35.5 1.0 CA A:GLU507 4.2 36.4 1.0 OP1 F:DA3 4.3 39.2 1.0 C A:ALA506 4.4 35.9 1.0 N A:THR447 4.6 36.3 1.0 CA A:ALA506 4.7 35.6 1.0 CB A:GLU507 4.7 36.5 1.0 O A:THR447 4.7 36.6 1.0 O A:VAL446 4.8 36.1 1.0 O5' F:DA3 4.8 37.4 1.0 N A:ILE508 4.9 35.1 1.0 CD1 A:TYR541 4.9 35.5 1.0 CE2 A:TYR541 5.0 35.7 1.0 O F:HOH26 5.0 26.3 1.0

Magnesium binding site 4 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg211 b:50.0 occ:1.00 O A:THR647 2.3 42.4 1.0 O A:VAL652 2.4 40.9 1.0 O A:LEU649 2.5 43.5 1.0 OP1 E:DA11 2.8 31.1 1.0 C A:THR647 3.3 42.0 1.0 C A:LEU649 3.4 43.1 1.0 C A:VAL652 3.4 41.1 1.0 N A:VAL652 3.7 41.2 1.0 C A:ASN648 3.8 42.3 1.0 P E:DA11 3.9 29.4 1.0 CA A:VAL652 3.9 40.8 1.0 N A:LEU649 3.9 42.3 1.0 OP2 E:DA11 4.1 31.7 1.0 CB A:VAL652 4.1 40.5 1.0 O A:ASN648 4.1 42.3 1.0 N A:GLY651 4.1 42.7 1.0 N A:ASN648 4.2 41.9 1.0 N A:PRO650 4.2 43.6 1.0 CA A:ASN648 4.2 42.2 1.0 CA A:THR647 4.3 42.1 1.0 CA A:LEU649 4.3 42.8 1.0 CA A:PRO650 4.3 43.2 1.0 N A:GLY653 4.5 41.6 1.0 C A:PRO650 4.6 43.0 1.0 O3' E:DT10 4.7 27.9 1.0 C A:GLY651 4.8 41.5 1.0 O A:VAL646 4.8 41.6 1.0 OG1 A:THR647 4.8 43.3 1.0 CG1 A:VAL652 4.9 39.8 1.0 CA A:GLY653 4.9 42.3 1.0

Magnesium binding site 5 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:34.9 occ:1.00 OD2 B:ASP570 2.2 45.6 1.0 O B:MET424 2.2 39.5 1.0 O2B B:DCP101 2.2 32.1 1.0 O1A B:DCP101 2.4 34.3 1.0 OD1 B:ASP423 2.4 41.1 1.0 O3G B:DCP101 2.5 40.5 1.0 CG B:ASP570 3.3 42.6 1.0 C B:MET424 3.4 38.7 1.0 PB B:DCP101 3.4 34.4 1.0 CG B:ASP423 3.6 40.2 1.0 PA B:DCP101 3.6 34.4 1.0 PG B:DCP101 3.7 39.1 1.0 O3A B:DCP101 3.8 34.3 1.0 OD1 B:ASP570 3.9 45.4 1.0 N B:MET424 3.9 37.9 1.0 NZ B:LYS625 3.9 47.0 1.0 O3B B:DCP101 3.9 37.1 1.0 C5' B:DCP101 4.1 38.6 1.0 CA B:MET424 4.1 38.7 1.0 OD2 B:ASP423 4.1 44.8 1.0 O2G B:DCP101 4.4 39.8 1.0 O5' B:DCP101 4.4 35.6 1.0 C B:ASP423 4.4 37.7 1.0 CB B:MET424 4.4 38.8 1.0 N B:ASP425 4.5 38.2 1.0 O B:ASP570 4.5 38.2 1.0 CB B:ASP570 4.5 40.3 1.0 CB B:PHE427 4.5 37.6 1.0 N B:CYS426 4.7 38.8 1.0 CA B:ASP425 4.7 38.5 1.0 N B:PHE427 4.7 37.8 1.0 O1B B:DCP101 4.7 35.7 1.0 CE B:LYS625 4.8 47.8 1.0 CB B:ASP423 4.8 38.2 1.0 C B:ASP425 4.8 38.5 1.0 OE1 B:GLU571 4.8 47.4 1.0 O2A B:DCP101 4.9 36.0 1.0 O1G B:DCP101 4.9 40.2 1.0 CA B:ASP423 4.9 37.8 1.0 O B:ASP423 4.9 37.8 1.0

Magnesium binding site 6 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg212 b:54.0 occ:1.00 O B:THR647 2.4 45.1 1.0 O B:LEU649 2.4 47.2 1.0 OP1 G:DA11 2.6 34.0 1.0 O B:VAL652 3.1 49.4 1.0 C B:LEU649 3.1 47.0 1.0 C B:THR647 3.5 45.5 1.0 C B:ASN648 3.5 46.6 1.0 N B:LEU649 3.6 46.4 1.0 N B:PRO650 3.7 47.6 1.0 O B:ASN648 3.8 46.7 1.0 CA B:ASN648 3.8 46.6 1.0 P G:DA11 3.9 34.0 1.0 CA B:LEU649 4.0 46.4 1.0 CA B:PRO650 4.0 47.7 1.0 C B:VAL652 4.1 48.8 1.0 N B:ASN648 4.1 46.0 1.0 N B:VAL652 4.1 48.4 1.0 OP2 G:DA11 4.2 34.6 1.0 N B:GLY651 4.3 47.9 1.0 C B:PRO650 4.4 47.8 1.0 CA B:VAL652 4.5 48.5 1.0 CB B:VAL652 4.6 48.6 1.0 CA B:THR647 4.6 45.5 1.0 O5' G:DA11 4.7 37.5 1.0 CD B:PRO650 4.8 48.0 1.0 OG1 B:THR647 4.9 46.9 1.0 O3' G:DT10 5.0 32.4 1.0

Magnesium binding site 7 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg205 b:25.3 occ:1.00 O2B C:DCP101 2.1 24.9 1.0 OD2 C:ASP570 2.2 35.6 1.0 O C:MET424 2.3 39.6 1.0 O3G C:DCP101 2.3 26.8 1.0 OD1 C:ASP423 2.3 41.9 1.0 O1A C:DCP101 2.4 29.0 1.0 PB C:DCP101 3.2 26.3 1.0 CG C:ASP570 3.4 35.2 1.0 CG C:ASP423 3.4 40.8 1.0 PG C:DCP101 3.5 26.6 1.0 C C:MET424 3.5 39.0 1.0 PA C:DCP101 3.5 29.2 1.0 O3A C:DCP101 3.6 26.6 1.0 O C:HOH87 3.7 46.2 1.0 O3B C:DCP101 3.7 24.9 1.0 MG C:MG206 3.8 33.1 0.5 NZ C:LYS625 3.8 32.2 1.0 O2G C:DCP101 3.9 30.4 1.0 OD1 C:ASP570 3.9 36.2 1.0 OD2 C:ASP423 3.9 43.7 1.0 N C:MET424 4.1 38.4 1.0 C5' C:DCP101 4.3 27.4 1.0 CA C:MET424 4.3 39.1 1.0 C C:ASP423 4.4 37.8 1.0 O5' C:DCP101 4.4 28.0 1.0 N C:CYS426 4.4 37.7 1.0 CE C:LYS625 4.5 34.0 1.0 N C:ASP425 4.5 39.0 1.0 O1B C:DCP101 4.6 26.6 1.0 N C:PHE427 4.6 33.7 1.0 CA C:ASP425 4.6 39.0 1.0 C C:ASP425 4.6 38.6 1.0 CB C:ASP570 4.6 33.5 1.0 CB C:PHE427 4.7 32.4 1.0 CB C:ASP423 4.7 38.0 1.0 CB C:MET424 4.7 39.2 1.0 O2A C:DCP101 4.8 28.0 1.0 O1G C:DCP101 4.8 26.7 1.0 O C:ASP423 4.9 37.6 1.0 CA C:ASP423 4.9 37.9 1.0 O C:ASP570 4.9 32.3 1.0 OE1 C:GLU571 5.0 35.0 1.0

Magnesium binding site 8 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg206 b:33.1 occ:0.50 OD1 C:ASP570 2.2 36.2 1.0 O1A C:DCP101 2.3 29.0 1.0 OE1 C:GLU571 2.4 35.0 1.0 C3' I:DOC12 3.1 35.2 1.0 CG C:ASP570 3.1 35.2 1.0 OG C:SER568 3.2 36.7 1.0 OD2 C:ASP570 3.4 35.6 1.0 PA C:DCP101 3.4 29.2 1.0 CD C:GLU571 3.5 34.5 1.0 CB C:GLU571 3.6 33.1 1.0 C5' C:DCP101 3.7 27.4 1.0 O C:HOH87 3.7 46.2 1.0 O5' C:DCP101 3.8 28.0 1.0 MG C:MG205 3.8 25.3 1.0 OD1 C:ASP423 3.8 41.9 1.0 O2A C:DCP101 3.9 28.0 1.0 C4' I:DOC12 4.0 36.7 1.0 CG C:GLU571 4.1 33.8 1.0 C2' I:DOC12 4.3 33.8 1.0 CB C:SER568 4.3 35.9 1.0 C5' I:DOC12 4.3 38.5 1.0 CG C:ASP423 4.5 40.8 1.0 CB C:ASP570 4.5 33.5 1.0 OE2 C:GLU571 4.5 37.4 1.0 OD2 C:ASP423 4.6 43.7 1.0 C C:ASP570 4.6 33.1 1.0 N C:GLU571 4.7 32.9 1.0 CA C:GLU571 4.7 33.1 1.0 O3A C:DCP101 4.8 26.6 1.0 O5' I:DOC12 4.9 42.3 1.0 O C:ASP570 4.9 32.3 1.0 O2B C:DCP101 4.9 24.9 1.0 N C:ASP570 4.9 34.1 1.0 CA C:ASP570 4.9 33.6 1.0

Magnesium binding site 9 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg213 b:44.4 occ:1.00 O C:THR647 2.3 36.9 1.0 O C:VAL652 2.4 32.1 1.0 O C:LEU649 2.5 34.8 1.0 OP1 I:DA11 2.5 32.3 1.0 C C:LEU649 3.4 34.4 1.0 C C:THR647 3.4 36.6 1.0 C C:VAL652 3.4 32.5 1.0 P I:DA11 3.7 30.2 1.0 N C:LEU649 3.9 34.8 1.0 N C:VAL652 3.9 32.0 1.0 C C:ASN648 3.9 35.6 1.0 OP2 I:DA11 4.0 34.3 1.0 CA C:ASN648 4.1 36.4 1.0 CA C:VAL652 4.1 31.7 1.0 N C:PRO650 4.1 34.5 1.0 N C:ASN648 4.1 36.4 1.0 CB C:VAL652 4.2 31.5 1.0 CA C:LEU649 4.2 34.5 1.0 CA C:PRO650 4.3 34.3 1.0 N C:GLY651 4.3 34.1 1.0 CA C:THR647 4.4 36.8 1.0 O C:ASN648 4.4 35.6 1.0 N C:GLY653 4.5 33.1 1.0 C C:PRO650 4.6 34.3 1.0 O3' I:DT10 4.7 30.4 1.0 O5' I:DA11 4.7 33.8 1.0 OG1 C:THR647 4.7 38.1 1.0 CA C:GLY653 4.9 33.9 1.0 C C:GLY651 4.9 32.7 1.0 O C:VAL646 5.0 37.0 1.0

Magnesium binding site 10 out of 13 in the Structure of Human REV1-Dna-Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Human REV1-Dna-Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg207 b:41.7 occ:1.00 O3G D:DCP101 2.0 40.8 1.0 O1A D:DCP101 2.2 36.8 1.0 O2B D:DCP101 2.3 35.9 1.0 O D:MET424 2.4 38.2 1.0 OD2 D:ASP423 2.4 40.5 1.0 OD2 D:ASP570 2.5 42.9 1.0 CG D:ASP423 3.3 39.4 1.0 PG D:DCP101 3.4 38.3 1.0 PB D:DCP101 3.4 37.7 1.0 MG D:MG208 3.5 60.6 1.0 PA D:DCP101 3.5 36.6 1.0 C D:MET424 3.5 38.0 1.0 CG D:ASP570 3.7 42.6 1.0 O3A D:DCP101 3.7 37.4 1.0 OD1 D:ASP423 3.7 42.0 1.0 O3B D:DCP101 3.8 38.6 1.0 NZ D:LYS625 3.9 44.4 1.0 N D:MET424 4.0 37.9 1.0 O2G D:DCP101 4.1 39.0 1.0 OD1 D:ASP570 4.1 44.5 1.0 C5' D:DCP101 4.2 38.4 1.0 CA D:MET424 4.3 38.5 1.0 O5' D:DCP101 4.4 37.6 1.0 CE D:LYS625 4.4 46.6 1.0 C D:ASP423 4.4 37.9 1.0 O1G D:DCP101 4.5 39.4 1.0 N D:ASP425 4.6 37.5 1.0 N D:CYS426 4.6 37.0 1.0 CB D:ASP423 4.6 37.9 1.0 O2A D:DCP101 4.7 39.7 1.0 CA D:ASP425 4.7 37.6 1.0 CB D:MET424 4.7 39.1 1.0 C D:ASP425 4.8 37.4 1.0 O1B D:DCP101 4.8 36.7 1.0 N D:PHE427 4.8 36.1 1.0 CA D:ASP423 4.8 37.6 1.0 CB D:ASP570 4.9 41.8 1.0 O D:ASP570 4.9 41.0 1.0 CB D:PHE427 5.0 35.8 1.0

M.K.Swan, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Structure of the Human REV1-Dna-Dntp Ternary Complex. J.Mol.Biol. V. 390 699 2009.
ISSN: ISSN 0022-2836
PubMed: 19464298
DOI: 10.1016/J.JMB.2009.05.026