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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

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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: Tue Jul 8 23:24:00 2025

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