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Calcium in PDB 4k4i: Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp.

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

All present enzymatic activity of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-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 (-)Ftc-Tp., PDB code: 4k4i 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) 45.03 / 2.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 194.440, 97.580, 105.150, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 27.4

Other elements in 4k4i:

The structure of Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-Tp. also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Arsenic (As) 2 atoms

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 (-)Ftc-Tp. (pdb code 4k4i). 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 (-)Ftc-Tp., PDB code: 4k4i:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 23 in 4k4i

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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 (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:33.8
occ:1.00
 O A:ALA344 2.3 20.0 1.0
O C:HOH103 2.3 29.3 1.0
OP1 C:DA5 2.4 22.0 1.0
O A:HOH828 2.4 24.2 1.0
O A:SER339 2.4 25.6 1.0
O A:ILE341 2.4 22.6 1.0
C A:ALA344 3.3 18.9 1.0
C A:ILE341 3.3 20.7 1.0
C A:SER339 3.4 23.2 1.0
P C:DA5 3.4 18.9 1.0
N A:ALA344 3.6 18.3 1.0
O C:HOH107 3.7 43.6 1.0
OP2 C:DA5 3.7 22.8 1.0
N A:GLY343 3.9 18.3 1.0
CA A:ALA344 3.9 18.3 1.0
CA A:SER339 4.0 28.0 1.0
CA A:TRP342 4.0 18.7 1.0
N A:TRP342 4.0 20.0 1.0
N A:ILE341 4.1 21.7 1.0
O3' C:DT4 4.2 20.9 1.0
C A:TRP342 4.3 19.1 1.0
N A:GLY345 4.3 20.6 1.0
C A:ASN340 4.3 23.6 1.0
CA A:ILE341 4.4 25.4 1.0
N A:ASN340 4.4 24.8 1.0
C A:GLY343 4.5 18.8 1.0
CB A:ALA344 4.5 17.2 1.0
CA A:GLY345 4.6 23.4 1.0
CA A:ASN340 4.6 26.0 1.0
O5' C:DA5 4.7 19.0 1.0
CB A:SER339 4.7 27.7 1.0
O A:PHE338 4.8 29.5 1.0
CA A:GLY343 4.8 17.8 1.0
O A:ASN340 4.9 22.9 1.0
O A:HOH782 4.9 38.2 1.0

Calcium binding site 2 out of 23 in 4k4i

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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 (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:53.7
occ:1.00
 O A:HOH822 2.3 45.1 1.0
O A:ILE305 2.3 39.9 1.0
O A:ILE302 2.4 36.2 1.0
O A:CYS300 2.4 40.6 1.0
OP1 D:DC3 2.4 39.5 1.0
C A:ILE302 3.3 33.5 1.0
C A:ILE305 3.4 35.3 1.0
C A:CYS300 3.5 31.0 1.0
P D:DC3 3.8 35.6 1.0
N A:ILE305 3.8 35.8 1.0
N A:PRO303 3.9 29.6 1.0
CA A:PRO303 3.9 29.4 1.0
N A:ILE302 4.1 32.9 1.0
C A:SER301 4.1 34.0 1.0
CA A:ILE305 4.1 35.4 1.0
N A:GLY304 4.2 29.5 1.0
CA A:ILE302 4.3 33.1 1.0
CA A:CYS300 4.3 32.0 1.0
O A:SER301 4.3 40.2 1.0
OP2 D:DC3 4.3 35.4 1.0
N A:GLY306 4.4 33.9 1.0
C A:PRO303 4.4 27.6 1.0
N A:SER301 4.5 33.0 1.0
O A:ALA299 4.6 27.2 1.0
CA A:SER301 4.6 33.3 1.0
CB A:ILE305 4.6 36.5 1.0
CA A:GLY306 4.7 32.6 1.0
O3' D:DC2 4.7 37.8 1.0
C A:GLY304 4.9 34.4 1.0

Calcium binding site 3 out of 23 in 4k4i

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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 (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:37.7
occ:1.00
 O A:HOH796 2.3 38.5 1.0
O A:SER463 2.3 20.6 1.0
O A:HOH827 2.3 30.6 1.0
O A:HOH777 2.3 30.9 1.0
O A:HOH757 2.4 35.6 1.0
C A:SER463 3.4 20.7 1.0
OP1 B:DT10 3.6 27.8 1.0
CA A:SER463 4.3 20.7 1.0
N A:SER463 4.3 20.5 1.0
N A:GLN464 4.4 19.9 1.0
CA A:GLN464 4.4 21.6 0.5
CB A:SER463 4.4 18.9 1.0
CA A:GLN464 4.4 19.8 0.5
N A:GLU465 4.5 19.6 1.0
OE2 A:GLU466 4.5 17.8 0.3
P B:DT10 4.6 26.6 1.0
NE2 A:GLN464 4.7 28.5 0.5
O A:HOH797 4.7 42.7 1.0
OP2 B:DT10 4.7 28.4 1.0
OE2 A:GLU465 4.9 26.5 1.0
OG A:SER463 4.9 21.1 1.0
OE1 A:GLU466 5.0 18.1 0.3

Calcium binding site 4 out of 23 in 4k4i

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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 (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:21.4
occ:1.00
 OD2 A:ASP429 2.3 21.4 1.0
OD1 A:ASP427 2.3 24.6 1.0
OAE A:1RY601 2.3 19.4 1.0
O A:HOH702 2.3 20.4 1.0
OAD A:1RY601 2.3 21.2 1.0
OAF A:1RY601 2.3 22.7 1.0
O A:ASP427 2.4 26.1 1.0
CG A:ASP429 3.3 23.2 1.0
PBB A:1RY601 3.4 20.5 1.0
CG A:ASP427 3.4 27.8 1.0
PBA A:1RY601 3.5 22.1 1.0
C A:ASP427 3.6 25.4 1.0
OD1 A:ASP429 3.6 22.4 1.0
PAZ A:1RY601 3.6 18.9 1.0
OAR A:1RY601 3.7 24.1 1.0
CA A:CA606 3.7 29.2 1.0
OAQ A:1RY601 3.9 18.7 1.0
N A:ASP427 4.1 23.6 1.0
OAC A:1RY601 4.1 20.6 1.0
O A:HOH736 4.1 36.8 1.0
CA A:ASP427 4.2 23.4 1.0
OG A:SER417 4.2 22.7 1.0
OD2 A:ASP427 4.2 35.8 1.0
O A:HOH703 4.2 17.7 1.0
N A:SER417 4.3 21.8 1.0
CA A:GLY416 4.3 20.2 1.0
CB A:ASP427 4.4 25.2 1.0
CAL A:1RY601 4.5 21.3 1.0
OAO A:1RY601 4.5 22.2 1.0
N A:VAL428 4.6 21.6 1.0
CB A:ASP429 4.7 19.7 1.0
OAI A:1RY601 4.8 21.1 1.0
OAH A:1RY601 4.8 24.2 1.0
N A:ASP429 4.8 18.5 1.0
OAG A:1RY601 4.8 18.2 1.0
C A:GLY416 4.9 21.0 1.0
CA A:VAL428 4.9 21.0 1.0
C A:VAL428 4.9 19.1 1.0

Calcium binding site 5 out of 23 in 4k4i

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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 (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca606

b:29.2
occ:1.00
 OD1 A:ASP429 2.3 22.4 1.0
OD2 A:ASP427 2.4 35.8 1.0
O3' C:DC6 2.4 33.6 1.0
OD2 A:ASP490 2.4 25.2 1.0
OAD A:1RY601 2.4 21.2 1.0
OD1 A:ASP427 2.4 24.6 1.0
CG A:ASP427 2.8 27.8 1.0
CG A:ASP429 3.4 23.2 1.0
PBA A:1RY601 3.6 22.1 1.0
CG A:ASP490 3.6 21.6 1.0
C3' C:DC6 3.7 27.6 1.0
CA A:CA605 3.7 21.4 1.0
OD2 A:ASP429 3.8 21.4 1.0
OAH A:1RY601 4.0 24.2 1.0
CB A:ASP427 4.4 25.2 1.0
O A:HOH736 4.4 36.8 1.0
CB A:ASP490 4.4 19.2 1.0
C5' C:DC6 4.5 21.8 1.0
C4' C:DC6 4.5 24.4 1.0
OAO A:1RY601 4.5 22.2 1.0
OD1 A:ASP490 4.5 23.1 1.0
CB A:ASP429 4.7 19.7 1.0
O A:ASP427 4.7 26.1 1.0
SAS A:1RY601 4.7 22.8 1.0
O5' C:DC6 4.8 19.8 1.0
OP1 C:DC6 4.9 22.4 1.0
CAL A:1RY601 4.9 21.3 1.0
C2' C:DC6 5.0 26.2 1.0
OAF A:1RY601 5.0 22.7 1.0
OAR A:1RY601 5.0 24.1 1.0

Calcium binding site 6 out of 23 in 4k4i

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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 (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca607

b:59.0
occ:1.00
 OE1 A:GLN400 2.3 45.7 1.0
O A:CYS412 2.3 34.4 1.0
OE2 A:GLU396 2.3 43.2 1.0
CD A:GLU396 3.3 38.8 1.0
C A:CYS412 3.4 28.9 1.0
CD A:GLN400 3.5 37.9 1.0
O A:HOH823 3.5 43.9 1.0
OE1 A:GLU396 3.7 51.1 1.0
NE2 A:GLN400 4.1 45.2 1.0
CA A:VAL413 4.1 26.8 1.0
N A:VAL413 4.2 27.2 1.0
CB A:CYS412 4.3 33.8 1.0
CA A:CYS412 4.4 30.8 1.0
CG A:GLU396 4.6 33.2 1.0
CG A:GLN400 4.6 35.6 1.0
CB A:GLN400 4.8 32.1 1.0
N A:CYS412 4.9 29.5 1.0
OE1 A:GLN397 5.0 60.3 1.0
CB A:VAL413 5.0 28.6 1.0

Calcium binding site 7 out of 23 in 4k4i

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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 (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca101

b:66.2
occ:1.00
 O B:HOH212 2.3 52.4 1.0
O B:HOH213 2.3 50.5 1.0
O B:HOH220 2.8 42.4 1.0
O6 B:DG3 4.4 36.2 1.0
N4 D:DC2 4.7 30.6 1.0
N7 B:DG2 4.7 35.4 1.0
O6 D:DG1 4.9 27.6 1.0
O6 B:DG2 4.9 35.9 1.0

Calcium binding site 8 out of 23 in 4k4i

Go back to Calcium Binding Sites List in 4k4i
Calcium binding site 8 out of 23 in the Ternary Crystal Structures of A Human Dna Polymerase Lambda in Complex with Dna and (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca602

b:30.5
occ:1.00
 OD1 E:ASP427 2.3 30.4 1.0
OAE E:1RY601 2.3 28.0 1.0
O E:HOH752 2.3 24.4 1.0
OAD E:1RY601 2.3 37.5 1.0
OD2 E:ASP429 2.3 36.9 1.0
OAF E:1RY601 2.3 28.3 1.0
O E:ASP427 3.3 32.6 1.0
CG E:ASP427 3.3 29.8 1.0
PBA E:1RY601 3.3 35.9 1.0
PBB E:1RY601 3.4 25.4 1.0
CG E:ASP429 3.4 38.6 1.0
PAZ E:1RY601 3.6 25.5 1.0
OAR E:1RY601 3.6 28.2 1.0
OD1 E:ASP429 3.7 38.3 1.0
CA E:CA603 3.7 51.0 1.0
OD2 E:ASP427 3.8 42.6 1.0
OAQ E:1RY601 3.8 28.1 1.0
C E:ASP427 4.0 28.5 1.0
O E:HOH754 4.0 47.8 1.0
OAC E:1RY601 4.1 23.3 1.0
N E:ASP427 4.3 23.5 1.0
O E:HOH701 4.3 29.1 1.0
OAO E:1RY601 4.4 36.3 1.0
N E:SER417 4.5 32.8 1.0
CA E:ASP427 4.5 27.2 1.0
CA E:GLY416 4.5 25.7 1.0
CB E:ASP427 4.5 29.2 1.0
OAH E:1RY601 4.5 36.8 1.0
CAL E:1RY601 4.5 36.8 1.0
OG E:SER417 4.6 30.6 1.0
OAI E:1RY601 4.7 28.3 1.0
OAG E:1RY601 4.8 24.9 1.0
CB E:ASP429 4.8 34.1 1.0
N E:VAL428 4.8 27.6 1.0

Calcium binding site 9 out of 23 in 4k4i

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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 (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca603

b:51.0
occ:1.00
 OD1 E:ASP429 2.3 38.3 1.0
OD2 E:ASP427 2.3 42.6 1.0
OD2 E:ASP490 2.4 44.9 1.0
OAD E:1RY601 2.4 37.5 1.0
CG E:ASP427 3.1 29.8 1.0
OD1 E:ASP427 3.2 30.4 1.0
CG E:ASP429 3.4 38.6 1.0
CG E:ASP490 3.7 36.2 1.0
OD2 E:ASP429 3.7 36.9 1.0
CA E:CA602 3.7 30.5 1.0
PBA E:1RY601 3.8 35.9 1.0
C3' G:DC6 4.0 32.8 1.0
OAH E:1RY601 4.1 36.8 1.0
O E:HOH754 4.1 47.8 1.0
C5' G:DC6 4.3 31.2 1.0
CB E:ASP427 4.5 29.2 1.0
OAO E:1RY601 4.5 36.3 1.0
SAS E:1RY601 4.5 33.8 1.0
O5' G:DC6 4.6 29.9 1.0
CB E:ASP490 4.6 29.5 1.0
OD1 E:ASP490 4.6 32.7 1.0
O3' G:DC6 4.7 44.0 1.0
CB E:ASP429 4.7 34.1 1.0
C4' G:DC6 4.7 31.8 1.0
C2' G:DC6 5.0 32.8 1.0

Calcium binding site 10 out of 23 in 4k4i

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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 (-)Ftc-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 (-)Ftc-Tp. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca604

b:64.3
occ:1.00
 O E:HOH778 2.3 40.9 1.0
O E:HOH754 2.3 47.8 1.0
OD2 E:ASP427 4.5 42.6 1.0
OAG E:1RY601 4.7 24.9 1.0
OAF E:1RY601 4.8 28.3 1.0
OP2 G:DC6 4.9 30.6 1.0
OAH E:1RY601 4.9 36.8 1.0
CG E:ASP427 5.0 29.8 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 08:52:25 2024

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