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Magnesium in PDB 6vdd: Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp

Enzymatic activity of Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp

All present enzymatic activity of Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp:
2.7.7.7;

Protein crystallography data

The structure of Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp, PDB code: 6vdd was solved by S.Shuman, Y.Goldgur, S.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.53 / 1.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 66.664, 233.805, 169.289, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp (pdb code 6vdd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp, PDB code: 6vdd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6vdd

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Magnesium binding site 1 out of 6 in the Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:44.5
occ:1.00
 O5' A:DCT1001 2.0 52.7 1.0
O A:HOH1287 2.1 41.8 1.0
O A:HOH1339 2.1 41.8 1.0
O3G A:DCT1001 2.1 49.9 1.0
O A:HOH1301 2.1 41.7 1.0
O2B A:DCT1001 2.2 44.0 1.0
PB A:DCT1001 3.2 40.8 1.0
PA A:DCT1001 3.2 49.7 1.0
PG A:DCT1001 3.3 48.8 1.0
O3A A:DCT1001 3.5 36.2 1.0
O A:HOH1236 3.6 65.7 1.0
O3B A:DCT1001 3.7 47.1 1.0
O A:HOH1146 3.7 56.1 1.0
OD2 A:ASP684 3.9 75.2 1.0
O2G A:DCT1001 3.9 34.4 1.0
O A:HOH1284 4.1 54.1 1.0
O2A A:DCT1001 4.2 57.4 1.0
O A:HOH1115 4.2 43.3 1.0
O B:HOH221 4.3 78.5 1.0
O1A A:DCT1001 4.4 54.1 1.0
N A:GLN687 4.4 34.3 1.0
O1G A:DCT1001 4.5 51.6 1.0
O1B A:DCT1001 4.6 38.7 1.0
CG A:ASP684 4.7 62.1 1.0
OD1 A:ASP684 4.7 74.1 1.0
OD2 A:ASP861 4.8 38.5 1.0
CA A:SER686 4.9 40.0 1.0

Magnesium binding site 2 out of 6 in 6vdd

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Magnesium binding site 2 out of 6 in the Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1003

b:54.0
occ:1.00
 O A:HOH1467 2.0 42.6 1.0
O A:HOH1495 2.0 44.7 1.0
O A:HOH1383 2.1 52.7 1.0
O A:HOH1211 2.3 34.1 1.0
O A:HOH1419 2.3 43.0 1.0
O A:HOH1234 4.1 42.6 1.0
O A:ASN625 4.2 35.0 1.0
O A:VAL627 4.4 31.5 1.0
O A:HOH1492 4.5 59.7 1.0
O A:LEU624 4.6 35.2 1.0
O A:HOH1445 4.6 73.9 1.0
CA A:ASN625 4.7 35.0 1.0
C A:ASN625 4.8 41.9 1.0
OD1 A:ASN625 5.0 45.4 1.0

Magnesium binding site 3 out of 6 in 6vdd

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Magnesium binding site 3 out of 6 in the Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:34.4
occ:1.00
 O A:HOH1428 2.0 32.4 1.0
O A:HOH1205 2.0 33.6 1.0
O C:HOH104 2.0 39.6 1.0
O A:ILE641 2.1 31.9 1.0
O A:HOH1413 2.2 35.0 1.0
O A:HOH1394 2.2 36.9 1.0
C A:ILE641 3.2 28.8 1.0
CA A:ILE641 3.7 24.4 1.0
OP1 C:DC11 4.0 36.1 1.0
O A:HOH1298 4.0 36.2 1.0
CG2 A:ILE641 4.0 26.5 1.0
O A:HOH1470 4.0 47.4 1.0
O A:GLN434 4.1 38.2 1.0
O A:GLY433 4.3 39.2 1.0
O A:PRO432 4.4 34.6 1.0
N A:ALA642 4.4 30.9 1.0
O C:HOH121 4.4 43.2 1.0
CB A:ILE641 4.5 28.1 1.0
O A:HOH1446 4.6 49.7 1.0
C A:GLY433 4.7 45.1 1.0
CA A:ALA642 4.7 33.0 1.0
N A:ALA643 4.7 32.5 1.0
O C:HOH102 4.8 44.0 1.0
CA A:GLY433 4.8 41.9 1.0
C A:GLN434 4.9 41.9 1.0
O A:THR640 4.9 32.2 1.0
N A:ILE641 4.9 25.5 1.0
C A:ALA642 4.9 38.5 1.0

Magnesium binding site 4 out of 6 in 6vdd

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Magnesium binding site 4 out of 6 in the Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg101

b:49.5
occ:1.00
 O A:HOH1367 2.1 49.0 1.0
O A:HOH1168 2.1 38.7 1.0
O A:HOH1385 2.3 60.1 1.0
OP1 B:DA11 2.3 40.8 1.0
O A:HOH1146 2.4 56.1 1.0
O B:HOH221 2.4 78.5 1.0
P B:DA11 3.6 35.4 1.0
C5' B:DA11 3.7 33.1 1.0
OE1 A:GLU862 3.8 52.0 1.0
O A:HOH1221 3.9 40.4 1.0
O5' B:DA11 4.0 34.2 1.0
OD1 A:ASP861 4.0 31.8 1.0
O A:HOH1339 4.1 41.8 1.0
O B:HOH210 4.2 44.6 1.0
OP2 B:DA11 4.5 33.5 1.0
O5' A:DCT1001 4.5 52.7 1.0
OD1 A:ASP684 4.5 74.1 1.0
OD2 A:ASP861 4.6 38.5 1.0
CD A:GLU862 4.6 51.3 1.0
CG A:ASP861 4.8 31.3 1.0
O3' B:DT10 4.8 32.4 1.0
CB A:GLU862 4.8 25.6 1.0
C4' B:DA11 4.9 37.1 1.0
CD1 A:ILE659 5.0 46.6 1.0
CG A:ASP684 5.0 62.1 1.0

Magnesium binding site 5 out of 6 in 6vdd

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Magnesium binding site 5 out of 6 in the Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1002

b:85.0
occ:1.00
 O2B D:DCT1001 2.3 94.6 1.0
O5' D:DCT1001 2.8 96.7 1.0
O3G D:DCT1001 3.4 87.0 1.0
N D:GLN687 3.6 34.0 1.0
PB D:DCT1001 3.7 84.4 1.0
O2G D:DCT1001 3.9 75.3 1.0
CA D:SER686 3.9 30.2 1.0
O D:TYR685 3.9 45.9 1.0
PG D:DCT1001 4.1 80.1 1.0
PA D:DCT1001 4.1 92.0 1.0
O D:HOH1153 4.2 48.5 1.0
C D:SER686 4.3 35.5 1.0
O3A D:DCT1001 4.4 88.3 1.0
O3B D:DCT1001 4.4 67.8 1.0
CB D:SER686 4.6 46.0 1.0
CA D:GLN687 4.6 38.2 1.0
CG D:GLN687 4.7 48.6 1.0
O1B D:DCT1001 4.8 62.4 1.0
C D:TYR685 4.8 38.5 1.0
N D:SER686 4.8 28.7 1.0
OG D:SER686 4.8 61.0 1.0

Magnesium binding site 6 out of 6 in 6vdd

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Magnesium binding site 6 out of 6 in the Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pol Domain of POL1 From M. Smegmatis Complex with Dna Primer-Template and Dntp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1003

b:42.6
occ:1.00
 O D:HOH1182 2.0 43.8 1.0
O D:HOH1336 2.0 33.8 1.0
O F:HOH105 2.1 39.5 1.0
O D:ILE641 2.2 35.3 1.0
O D:HOH1354 2.2 39.0 1.0
O D:HOH1270 2.3 50.9 1.0
C D:ILE641 3.3 35.9 1.0
CA D:ILE641 3.9 28.7 1.0
OP1 F:DC11 4.0 39.9 1.0
O D:GLN434 4.0 44.1 1.0
O D:HOH1169 4.0 40.6 1.0
CG2 D:ILE641 4.2 32.6 1.0
O D:GLY433 4.2 38.6 1.0
O D:HOH1360 4.3 47.4 1.0
O D:PRO432 4.4 35.4 1.0
O F:HOH123 4.4 45.6 1.0
O F:HOH111 4.4 44.2 1.0
N D:ALA642 4.4 32.0 1.0
C D:GLY433 4.6 47.6 1.0
CB D:ILE641 4.7 30.7 1.0
CA D:ALA642 4.8 31.2 1.0
N D:ALA643 4.8 36.9 1.0
C D:GLN434 4.8 49.0 1.0
CA D:GLY433 4.8 44.3 1.0
C D:ALA642 4.9 35.3 1.0
CA D:ARG435 5.0 69.4 1.0

Reference:

S.Ghosh, Y.Goldgur, S.Shuman. Mycobacterial Dna Polymerase I: Activities and Crystal Structures of the Pol Domain As Apoenzyme and in Complex with A Dna Primer-Template and of the Full-Length Fen/Exo-Pol Enzyme Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962
Page generated: Tue Oct 1 22:00:16 2024

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