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Calcium in PDB 5b2p: Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)

Protein crystallography data

The structure of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam), PDB code: 5b2p was solved by H.Hirano, H.Nishimasu, T.Nakane, R.Ishitani, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.26 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.611, 159.273, 96.674, 90.00, 106.86, 90.00
R / Rfree (%) 18 / 20.3

Other elements in 5b2p:

The structure of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
Sodium (Na) 4 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) (pdb code 5b2p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam), PDB code: 5b2p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 17 in 5b2p

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Calcium binding site 1 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1706

b:67.1
occ:1.00
O A:HOH1883 2.3 48.2 1.0
ND1 A:HIS1162 2.4 41.7 1.0
O A:HOH1839 2.5 58.2 1.0
OD2 A:ASP11 2.6 55.2 1.0
OE2 A:GLU903 2.8 39.2 0.4
OE1 A:GLU903 2.9 44.8 0.4
OD1 A:ASP11 3.0 49.9 1.0
OE2 A:GLU903 3.1 45.6 0.6
CE1 A:HIS1162 3.2 41.9 1.0
CD A:GLU903 3.2 42.7 0.4
CG A:ASP11 3.2 50.4 1.0
CG A:HIS1162 3.5 41.8 1.0
O A:HOH1923 3.6 58.1 1.0
CB A:HIS1162 3.9 39.4 1.0
CA A:HIS1162 4.1 39.5 1.0
CD A:GLU903 4.2 45.2 0.6
O A:HOH2168 4.3 56.6 1.0
NE2 A:HIS1162 4.4 46.9 1.0
OD2 A:ASP1165 4.4 43.5 1.0
OE1 A:GLN1157 4.5 63.6 1.0
NE2 A:GLN1157 4.5 59.0 1.0
O A:ASN16 4.5 39.5 1.0
CD2 A:HIS1162 4.5 44.8 1.0
CG A:GLU903 4.7 41.6 0.4
CB A:ASP11 4.8 42.6 1.0
OE1 A:GLU903 4.8 43.3 0.6
O A:ASP11 4.9 38.0 1.0
CD A:GLN1157 4.9 62.9 1.0

Calcium binding site 2 out of 17 in 5b2p

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Calcium binding site 2 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1707

b:34.4
occ:1.00
O B:HOH503 2.4 40.9 1.0
OP2 B:A60 2.4 30.3 1.0
O B:HOH322 2.4 31.1 1.0
O A:HOH2357 2.4 42.8 1.0
OD2 A:ASP66 2.5 30.9 1.0
O B:HOH317 2.5 35.0 1.0
O B:HOH408 2.6 42.8 1.0
O B:HOH332 3.6 29.1 1.0
CG A:ASP66 3.6 28.0 1.0
P B:A60 3.7 28.8 1.0
O B:HOH338 4.0 51.3 1.0
OD1 A:ASP66 4.0 24.9 1.0
O B:HOH273 4.1 33.3 1.0
O6 B:G62 4.2 22.9 1.0
OP1 B:A60 4.2 26.3 1.0
O5' B:A60 4.3 29.9 1.0
CA A:CA1709 4.3 51.0 1.0
N7 B:A61 4.6 25.6 1.0
O2 B:EDO111 4.7 27.1 1.0
CB A:ASP66 4.8 23.5 1.0
OP2 B:A61 4.8 25.8 1.0
O B:HOH276 4.9 24.5 1.0
N7 B:A60 4.9 35.0 1.0
O B:HOH206 5.0 43.5 1.0
O3' B:A59 5.0 28.9 1.0

Calcium binding site 3 out of 17 in 5b2p

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Calcium binding site 3 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1708

b:42.3
occ:1.00
O A:HOH2409 2.2 54.5 1.0
O A:HOH1984 2.3 30.4 1.0
O C:HOH264 2.3 55.2 1.0
O A:HOH2401 2.4 49.3 1.0
O A:HOH1808 2.4 41.3 1.0
O C:HOH210 2.5 39.3 1.0
O C:HOH229 2.6 34.8 1.0
O C:HOH252 3.7 42.8 1.0
OP1 C:DC18 4.2 33.2 1.0
OD2 A:ASP451 4.4 31.3 1.0
O B:HOH454 4.4 53.3 1.0
OD1 A:ASP451 4.5 25.5 1.0
CG A:LYS808 4.5 41.1 1.0
OP1 C:DG17 4.6 30.2 1.0
O A:HOH1845 4.7 57.6 1.0
OP2 C:DC18 4.8 31.3 1.0
OE1 A:GLN663 4.8 35.1 0.6
P C:DC18 4.8 29.2 1.0
O A:HOH1891 4.8 52.6 1.0
CG A:ASP451 4.9 28.4 1.0

Calcium binding site 4 out of 17 in 5b2p

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Calcium binding site 4 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1709

b:51.0
occ:1.00
O B:HOH303 2.3 28.7 1.0
OD1 A:ASP66 2.3 24.9 1.0
O A:HOH1818 2.3 20.3 1.0
O B:HOH338 2.3 51.3 1.0
O B:HOH525 2.5 57.5 1.0
O B:HOH408 2.5 42.8 1.0
O B:HOH284 2.7 26.0 1.0
O B:HOH377 2.7 26.4 1.0
CG A:ASP66 3.4 28.0 1.0
OD2 A:ASP66 3.7 30.9 1.0
O A:HOH2357 3.7 42.8 1.0
O B:HOH206 4.1 43.5 1.0
O B:HOH421 4.2 26.1 1.0
O B:HOH317 4.2 35.0 1.0
OE1 A:GLN69 4.3 27.0 1.0
CA A:CA1707 4.3 34.4 1.0
OP1 B:U52 4.4 23.3 1.0
OP1 B:C53 4.4 24.7 1.0
O A:HOH2242 4.6 35.2 1.0
O6 B:G62 4.6 22.9 1.0
CB A:ASP66 4.7 23.5 1.0
OP2 B:U52 4.8 23.2 1.0
CG2 A:ILE65 4.9 26.5 1.0
O A:ARG62 4.9 21.6 1.0
CA A:ASP66 5.0 23.4 1.0

Calcium binding site 5 out of 17 in 5b2p

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Calcium binding site 5 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1710

b:49.0
occ:1.00
OP1 B:U83 2.2 46.4 1.0
O A:VAL402 2.3 34.7 1.0
O B:HOH490 2.4 48.9 1.0
O A:HOH2358 2.5 35.0 1.0
O B:HOH499 2.6 66.1 1.0
O A:HOH2319 2.9 45.1 1.0
C A:VAL402 3.5 35.3 1.0
P B:U83 3.5 42.0 1.0
O3' B:U82 4.1 34.5 1.0
N A:VAL402 4.2 30.4 1.0
O5' B:U83 4.3 51.7 1.0
CA A:VAL402 4.4 33.5 1.0
N A:GLY403 4.4 34.7 1.0
CA A:GLY403 4.4 35.8 1.0
O A:HOH2047 4.5 29.4 1.0
C6 B:U83 4.5 73.4 1.0
OP2 B:U83 4.5 43.6 1.0
C5 B:U83 4.6 74.9 1.0
O B:HOH483 4.7 51.5 1.0
CB A:VAL402 4.8 34.5 1.0
O A:HOH2156 4.9 35.8 1.0

Calcium binding site 6 out of 17 in 5b2p

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Calcium binding site 6 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1711

b:79.0
occ:1.00
O A:HOH2439 2.3 45.0 1.0
O B:HOH296 2.5 48.9 1.0
O A:HOH1880 2.6 56.7 1.0
O B:HOH496 2.8 57.2 1.0
O B:HOH325 2.8 51.0 1.0
O A:HOH1893 2.8 41.6 1.0
OP1 B:G41 4.3 36.9 1.0
OD2 A:ASP1297 4.4 36.7 1.0
OP2 B:G28 4.5 30.0 1.0
OD1 A:ASP1297 4.7 35.9 1.0
O B:HOH209 4.9 42.1 1.0
O B:HOH360 4.9 41.7 1.0
CG A:ASP1297 4.9 35.7 1.0

Calcium binding site 7 out of 17 in 5b2p

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Calcium binding site 7 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1712

b:61.4
occ:1.00
O B:HOH278 2.4 43.0 1.0
O A:SER507 2.4 35.1 1.0
O B:HOH423 2.5 63.7 1.0
O A:HOH2369 2.5 49.1 1.0
O A:HOH2367 2.6 85.0 1.0
C A:SER507 3.7 34.2 1.0
O4 B:U84 4.2 86.9 1.0
O A:HOH2288 4.3 49.0 1.0
CA A:SER507 4.5 29.6 1.0
CB A:SER507 4.6 28.8 1.0
N A:LYS508 4.6 32.9 1.0
O A:HOH1871 4.6 30.0 1.0
O4 B:U82 4.6 34.6 1.0
O B:HOH366 4.7 46.4 1.0
CA A:LYS508 4.7 36.0 1.0
O B:HOH385 4.7 29.3 1.0
OD2 A:ASP509 4.7 49.5 0.4
C4 B:U84 4.9 85.6 1.0

Calcium binding site 8 out of 17 in 5b2p

Go back to Calcium Binding Sites List in 5b2p
Calcium binding site 8 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1713

b:96.6
occ:1.00
O A:HOH2379 2.6 72.9 1.0
O A:LYS1415 2.7 43.0 1.0
O A:HOH2141 2.8 46.7 1.0
OD1 A:ASP1417 2.8 38.8 1.0
O A:HOH2386 3.1 55.9 1.0
C A:LYS1415 3.8 43.0 1.0
CG A:ASP1417 3.8 37.8 1.0
O A:HOH2218 3.9 36.7 1.0
CA A:LYS1415 4.3 46.3 1.0
OD2 A:ASP1417 4.4 39.7 1.0
O A:HOH2182 4.5 41.2 1.0
NE1 A:TRP1409 4.6 32.3 1.0
N A:ASP1417 4.6 38.4 1.0
O A:ILE1414 4.7 47.8 1.0
N A:ASP1416 4.9 39.6 1.0
CA A:ASP1417 4.9 36.5 1.0
CB A:ASP1417 5.0 34.8 1.0
C A:ASP1416 5.0 37.8 1.0

Calcium binding site 9 out of 17 in 5b2p

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Calcium binding site 9 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1714

b:60.6
occ:1.00
O A:HOH2045 2.5 50.7 1.0
O A:HOH1846 2.5 44.2 1.0
O A:HOH2078 2.5 35.5 1.0
O C:HOH204 2.6 44.2 1.0
O C:HOH258 2.6 58.8 1.0
O B:HOH250 2.7 49.9 1.0
O A:HOH2195 2.8 45.5 1.0
NZ A:LYS664 4.1 48.1 1.0
OP2 B:A6 4.3 36.2 1.0
O A:ASN810 4.4 28.2 1.0
OP2 C:DC20 4.4 34.3 1.0
OD1 A:ASN812 4.4 36.8 1.0
O C:HOH207 4.4 49.0 1.0
O C:HOH212 4.5 40.3 1.0
CE A:LYS664 4.7 44.6 1.0
CB A:ASN812 4.7 27.4 1.0
CG A:ASN812 4.7 35.4 1.0
O C:HOH216 4.8 46.8 1.0
OP1 B:A6 4.9 34.9 1.0

Calcium binding site 10 out of 17 in 5b2p

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Calcium binding site 10 out of 17 in the Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Francisella Novicida CAS9 in Complex with Sgrna and Target Dna (Tga Pam) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1715

b:52.0
occ:1.00
OE1 A:GLU1231 2.6 45.2 1.0
OG A:SER1499 2.8 35.8 1.0
N A:SER1499 3.0 34.3 1.0
OD1 A:ASN1234 3.3 37.1 1.0
CD A:GLU1231 3.4 47.7 1.0
CB A:SER1499 3.4 32.3 1.0
O A:HOH1965 3.5 38.2 1.0
N A:ASP1498 3.5 35.9 1.0
CA A:SER1499 3.8 33.1 1.0
OE2 A:GLU1231 3.8 48.1 1.0
CB A:ILE1497 3.8 35.7 1.0
C A:ASP1498 3.9 33.8 1.0
CB A:ASP1498 3.9 34.5 1.0
CA A:ASP1498 3.9 35.7 1.0
CD1 A:ILE1497 3.9 33.0 1.0
CG1 A:ILE1497 4.0 34.4 1.0
ND2 A:ASN1234 4.1 27.3 1.0
CG A:ASN1234 4.2 31.7 1.0
C A:ILE1497 4.2 30.4 1.0
CG A:GLU1231 4.5 48.0 1.0
CA A:ILE1497 4.5 35.0 1.0
CA A:GLU1231 4.6 38.2 1.0
N A:GLY1232 4.8 37.5 1.0
CG A:ASP1498 4.9 40.9 1.0
O A:ILE1497 4.9 30.3 1.0
CG2 A:ILE1497 4.9 36.1 1.0
CB A:GLU1231 5.0 42.0 1.0

Reference:

H.Hirano, J.S.Gootenberg, T.Horii, O.O.Abudayyeh, M.Kimura, P.D.Hsu, T.Nakane, R.Ishitani, I.Hatada, F.Zhang, H.Nishimasu, O.Nureki. Structure and Engineering of Francisella Novicida CAS9 Cell V. 164 950 2016.
ISSN: ISSN 1097-4172
PubMed: 26875867
DOI: 10.1016/J.CELL.2016.01.039
Page generated: Sat Dec 12 05:18:08 2020

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