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Calcium in PDB 4k4h: Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.

Enzymatic activity of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.

All present enzymatic activity of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.:
2.7.7.7;

Protein crystallography data

The structure of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp., PDB code: 4k4h was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.88 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 194.950, 97.440, 105.170, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 26

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Calcium atom in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. (pdb code 4k4h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 23 binding sites of Calcium where determined in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp., PDB code: 4k4h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 23 in 4k4h

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Calcium binding site 1 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:24.3
occ:1.00
 O A:HOH707 2.3 22.3 1.0
O2C A:1RZ601 2.3 25.2 1.0
OD2 A:ASP429 2.3 24.4 1.0
OD1 A:ASP427 2.3 24.0 1.0
O2B A:1RZ601 2.3 22.0 1.0
O2A A:1RZ601 2.4 21.9 1.0
O A:ASP427 2.4 33.3 1.0
CG A:ASP429 3.3 27.3 1.0
PB A:1RZ601 3.4 22.1 1.0
CG A:ASP427 3.5 29.2 1.0
C A:ASP427 3.5 28.3 1.0
PA A:1RZ601 3.6 25.6 1.0
PG A:1RZ601 3.6 23.2 1.0
OD1 A:ASP429 3.6 28.7 1.0
CA A:CA604 3.7 29.0 1.0
O3A A:1RZ601 3.8 24.7 1.0
O3B A:1RZ601 3.9 24.3 1.0
N A:ASP427 4.0 26.3 1.0
O3G A:1RZ601 4.0 24.1 1.0
CA A:ASP427 4.2 28.0 1.0
OG A:SER417 4.2 25.7 1.0
OD2 A:ASP427 4.3 37.8 1.0
O A:HOH708 4.3 24.1 1.0
N A:SER417 4.4 26.0 1.0
CA A:GLY416 4.4 23.4 1.0
CB A:ASP427 4.4 27.6 1.0
O5' A:1RZ601 4.5 23.4 1.0
C5' A:1RZ601 4.5 24.5 1.0
N A:VAL428 4.6 25.2 1.0
CB A:ASP429 4.7 23.2 1.0
O1G A:1RZ601 4.8 20.4 1.0
O1A A:1RZ601 4.8 25.9 1.0
O1B A:1RZ601 4.8 24.1 1.0
CA A:VAL428 4.9 25.3 1.0
N A:ASP429 4.9 19.9 1.0
O A:HOH752 4.9 32.2 1.0
C A:VAL428 5.0 21.0 1.0
C A:GLY416 5.0 25.1 1.0

Calcium binding site 2 out of 23 in 4k4h

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Calcium binding site 2 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:46.2
occ:1.00
 O B:HOH206 2.3 33.4 1.0
O A:HOH812 2.3 37.3 1.0
O A:HOH813 2.3 47.7 1.0
O A:HOH774 2.3 32.8 1.0
O A:SER463 2.3 24.2 1.0
C A:SER463 3.5 23.4 1.0
OP1 B:DT10 3.5 28.6 1.0
CA A:GLN464 4.3 21.9 1.0
N A:GLN464 4.4 21.1 1.0
CA A:SER463 4.4 22.7 1.0
N A:GLU465 4.4 23.6 1.0
N A:SER463 4.4 22.3 1.0
CB A:SER463 4.5 21.0 1.0
OE2 A:GLU466 4.5 45.8 1.0
P B:DT10 4.6 29.2 1.0
OE1 A:GLU466 4.6 37.8 1.0
OP2 B:DT10 4.6 30.1 1.0
OG A:SER463 4.9 22.2 1.0
OE2 A:GLU465 4.9 26.5 1.0
C A:GLN464 5.0 21.9 1.0

Calcium binding site 3 out of 23 in 4k4h

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Calcium binding site 3 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:29.0
occ:1.00
 OD1 A:ASP429 2.3 28.7 1.0
O A:HOH752 2.3 32.2 1.0
OD2 A:ASP427 2.4 37.8 1.0
O3' C:DC6 2.4 42.8 1.0
OD2 A:ASP490 2.4 26.6 1.0
O2A A:1RZ601 2.4 21.9 1.0
OD1 A:ASP427 2.5 24.0 1.0
CG A:ASP427 2.8 29.2 1.0
CG A:ASP429 3.4 27.3 1.0
CG A:ASP490 3.6 22.9 1.0
PA A:1RZ601 3.6 25.6 1.0
OD2 A:ASP429 3.7 24.4 1.0
C3' C:DC6 3.7 31.4 1.0
CA A:CA602 3.7 24.3 1.0
O1A A:1RZ601 4.0 25.9 1.0
CB A:ASP490 4.3 19.2 1.0
CB A:ASP427 4.4 27.6 1.0
O5' A:1RZ601 4.4 23.4 1.0
OD1 A:ASP490 4.5 21.5 1.0
C4' C:DC6 4.5 25.5 1.0
C5' C:DC6 4.6 23.1 1.0
O A:ASP427 4.8 33.3 1.0
CB A:ASP429 4.8 23.2 1.0
OP1 C:DC6 4.8 23.6 1.0
O5' C:DC6 4.8 22.1 1.0
NH2 A:ARG488 4.8 23.8 1.0
O C:HOH110 4.8 34.7 1.0
S3' A:1RZ601 4.8 23.9 1.0
C2' C:DC6 4.9 29.7 1.0
O2C A:1RZ601 5.0 25.2 1.0

Calcium binding site 4 out of 23 in 4k4h

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Calcium binding site 4 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:33.6
occ:1.00
 O A:ALA344 2.3 21.8 1.0
O C:HOH111 2.3 28.9 1.0
OP1 C:DA5 2.4 20.3 1.0
O C:HOH101 2.4 24.3 1.0
O A:ILE341 2.4 22.6 1.0
O A:SER339 2.4 23.9 1.0
C A:ALA344 3.3 19.0 1.0
C A:ILE341 3.3 21.7 1.0
P C:DA5 3.4 19.4 1.0
C A:SER339 3.4 23.9 1.0
OP2 C:DA5 3.6 21.8 1.0
N A:ALA344 3.6 20.3 1.0
O C:HOH105 3.6 39.5 1.0
N A:GLY343 4.0 17.0 1.0
CA A:ALA344 4.0 19.8 1.0
CA A:TRP342 4.1 20.1 1.0
N A:TRP342 4.1 21.0 1.0
CA A:SER339 4.1 30.1 1.0
N A:ILE341 4.1 25.4 1.0
O3' C:DT4 4.2 21.5 1.0
N A:GLY345 4.3 22.9 1.0
CA A:ILE341 4.3 26.7 1.0
C A:TRP342 4.4 20.6 1.0
C A:ASN340 4.4 25.0 1.0
N A:ASN340 4.5 25.8 1.0
CA A:GLY345 4.5 26.7 1.0
C A:GLY343 4.5 18.9 1.0
CB A:ALA344 4.6 17.9 1.0
CA A:ASN340 4.6 25.0 1.0
O5' C:DA5 4.7 18.0 1.0
CA A:GLY343 4.8 17.1 1.0
O A:PHE338 4.8 29.0 1.0
CB A:SER339 4.9 30.4 1.0

Calcium binding site 5 out of 23 in 4k4h

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Calcium binding site 5 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:62.4
occ:1.00
 OE1 A:GLN400 2.3 42.4 1.0
OE2 A:GLU396 2.3 49.9 1.0
O A:CYS412 2.4 31.9 1.0
O A:HOH806 3.2 47.1 1.0
CD A:GLN400 3.4 38.1 1.0
C A:CYS412 3.4 31.6 1.0
CD A:GLU396 3.4 41.8 1.0
OE1 A:GLU396 3.9 50.3 1.0
NE2 A:GLN400 4.0 46.9 1.0
CB A:CYS412 4.2 33.4 1.0
CA A:VAL413 4.2 29.0 1.0
N A:VAL413 4.3 31.9 1.0
CA A:CYS412 4.3 31.7 1.0
CG A:GLN400 4.5 34.7 1.0
N A:CYS412 4.6 30.3 1.0
CG A:GLU396 4.7 35.6 1.0
CB A:GLN400 4.7 32.5 1.0
OE1 A:GLN397 4.8 58.9 1.0
CB A:VAL413 5.0 33.1 1.0

Calcium binding site 6 out of 23 in 4k4h

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Calcium binding site 6 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:51.9
occ:1.00
 O A:HOH701 2.3 43.5 1.0
O A:HOH732 2.3 36.6 1.0
O A:ILE305 2.4 41.0 1.0
O A:ILE302 2.4 35.6 1.0
O A:CYS300 2.4 40.6 1.0
OP1 D:DC3 2.4 39.4 1.0
C A:ILE302 3.3 34.0 1.0
C A:ILE305 3.5 33.9 1.0
C A:CYS300 3.6 34.1 1.0
P D:DC3 3.7 34.6 1.0
CA A:PRO303 3.8 38.4 1.0
N A:ILE305 3.9 34.8 1.0
N A:PRO303 4.0 36.8 1.0
OP2 D:DC3 4.1 32.8 1.0
N A:ILE302 4.2 36.0 1.0
CA A:ILE305 4.2 32.6 1.0
C A:SER301 4.2 39.8 1.0
N A:GLY304 4.3 33.3 1.0
O A:SER301 4.3 42.2 1.0
CA A:ILE302 4.3 35.3 1.0
CA A:CYS300 4.4 35.2 1.0
C A:PRO303 4.4 35.9 1.0
N A:GLY306 4.5 34.5 1.0
N A:SER301 4.6 34.1 1.0
O3' D:DC2 4.6 34.6 1.0
CB A:ILE305 4.7 34.2 1.0
CA A:SER301 4.7 36.8 1.0
O A:ALA299 4.8 35.1 1.0
CA A:GLY306 4.8 31.8 1.0
C A:GLY304 4.9 37.4 1.0

Calcium binding site 7 out of 23 in 4k4h

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Calcium binding site 7 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:65.1
occ:1.00
 O B:HOH202 2.3 44.9 1.0
O B:HOH203 2.3 51.3 1.0
N4 D:DC2 4.3 34.2 1.0
O6 B:DG3 4.4 32.1 1.0
N7 B:DG2 4.4 38.2 1.0
O6 B:DG2 4.6 32.9 1.0
O6 D:DG1 4.9 29.0 1.0

Calcium binding site 8 out of 23 in 4k4h

Go back to Calcium Binding Sites List in 4k4h
Calcium binding site 8 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca602

b:26.6
occ:1.00
 O2A E:1RZ601 2.3 34.4 1.0
OD1 E:ASP427 2.3 32.0 1.0
O E:HOH709 2.3 30.2 1.0
OD1 E:ASP429 2.3 38.0 1.0
O2C E:1RZ601 2.3 25.9 1.0
O2B E:1RZ601 2.4 23.0 1.0
O E:ASP427 3.3 33.5 1.0
CG E:ASP427 3.3 34.0 1.0
CG E:ASP429 3.4 38.7 1.0
PA E:1RZ601 3.4 42.6 1.0
PB E:1RZ601 3.5 25.7 1.0
CA E:CA604 3.5 53.0 1.0
PG E:1RZ601 3.5 26.4 1.0
OD2 E:ASP429 3.7 40.7 1.0
O3A E:1RZ601 3.8 27.7 1.0
C E:ASP427 3.9 33.4 1.0
O3B E:1RZ601 3.9 27.2 1.0
OD2 E:ASP427 4.0 44.8 1.0
N E:ASP427 4.1 28.8 1.0
O3G E:1RZ601 4.1 24.1 1.0
CA E:ASP427 4.4 31.0 1.0
O5' E:1RZ601 4.4 40.1 1.0
CB E:ASP427 4.4 32.2 1.0
N E:SER417 4.4 32.7 1.0
OG E:SER417 4.5 28.7 1.0
O E:HOH704 4.5 30.1 1.0
CA E:GLY416 4.5 28.4 1.0
O1A E:1RZ601 4.5 39.8 1.0
C5' E:1RZ601 4.6 37.8 1.0
O1G E:1RZ601 4.7 23.9 1.0
N E:VAL428 4.7 29.9 1.0
CB E:ASP429 4.8 33.8 1.0
O1B E:1RZ601 4.9 27.1 1.0
N E:ASP429 4.9 28.2 1.0

Calcium binding site 9 out of 23 in 4k4h

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Calcium binding site 9 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca603

b:39.7
occ:1.00
 O E:SER339 2.3 29.8 1.0
O E:ALA344 2.3 30.7 1.0
OP1 G:DA5 2.4 26.0 1.0
O E:HOH732 2.4 36.2 1.0
O G:HOH101 2.4 33.0 1.0
O E:ILE341 2.4 26.0 1.0
C E:SER339 3.3 25.6 1.0
C E:ILE341 3.4 28.6 1.0
P G:DA5 3.4 28.6 1.0
C E:ALA344 3.4 30.4 1.0
OP2 G:DA5 3.6 32.7 1.0
N E:ALA344 3.8 26.2 1.0
CA E:SER339 3.9 26.9 1.0
O G:HOH102 3.9 39.0 1.0
N E:GLY343 4.0 23.6 1.0
CA E:TRP342 4.0 26.4 1.0
N E:ILE341 4.1 28.2 1.0
CA E:ALA344 4.1 28.0 1.0
N E:TRP342 4.2 26.5 1.0
C E:ASN340 4.3 29.1 1.0
C E:TRP342 4.3 24.7 1.0
N E:ASN340 4.3 27.4 1.0
O3' G:DT4 4.4 27.1 1.0
CB E:SER339 4.4 27.4 1.0
CA E:ILE341 4.4 27.8 1.0
N E:GLY345 4.4 33.3 1.0
CA E:ASN340 4.5 27.4 1.0
CA E:GLY345 4.6 31.3 1.0
O5' G:DA5 4.7 26.5 1.0
CB E:ALA344 4.7 24.9 1.0
C E:GLY343 4.7 23.0 1.0
CA E:GLY343 4.9 23.2 1.0
O E:ASN340 5.0 30.3 1.0

Calcium binding site 10 out of 23 in 4k4h

Go back to Calcium Binding Sites List in 4k4h
Calcium binding site 10 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)3TC-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca604

b:53.0
occ:1.00
 OD2 E:ASP429 2.4 40.7 1.0
OD2 E:ASP427 2.4 44.8 1.0
OD2 E:ASP490 2.4 40.0 1.0
OD1 E:ASP427 2.4 32.0 1.0
O2A E:1RZ601 2.4 34.4 1.0
CG E:ASP427 2.7 34.0 1.0
CG E:ASP429 3.2 38.7 1.0
OD1 E:ASP429 3.5 38.0 1.0
CA E:CA602 3.5 26.6 1.0
CG E:ASP490 3.7 36.5 1.0
PA E:1RZ601 3.7 42.6 1.0
O1A E:1RZ601 4.0 39.8 1.0
CB E:ASP427 4.2 32.2 1.0
C3' G:DC6 4.2 35.0 1.0
O3' G:DC6 4.3 50.6 1.0
O5' E:1RZ601 4.4 40.1 1.0
OD1 E:ASP490 4.5 36.5 1.0
CB E:ASP490 4.6 29.4 1.0
CB E:ASP429 4.7 33.8 1.0
S3' E:1RZ601 4.8 33.6 1.0
O2C E:1RZ601 4.8 25.9 1.0
C5' G:DC6 4.8 35.6 1.0
O5' G:DC6 5.0 31.5 1.0
O E:VAL428 5.0 26.5 1.0

Reference:

R.Vyas, W.J.Zahurancik, Z.Suo. Structural Basis For the Binding and Incorporation of Nucleotide Analogs with L-Stereochemistry By Human Dna Polymerase Lambda. Proc.Natl.Acad.Sci.Usa V. 111 E3033 2014.
ISSN: ISSN 0027-8424
PubMed: 25015085
DOI: 10.1073/PNAS.1401286111
Page generated: Sun Jul 14 08:52:15 2024

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