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Calcium in PDB 5zac: Crystal Structure of Cona-R2M

Protein crystallography data

The structure of Crystal Structure of Cona-R2M, PDB code: 5zac was solved by J.H.Gan, G.S.Chen, R.T.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.227, 119.893, 125.211, 90.00, 90.00, 90.00
R / Rfree (%) 27.8 / 37.2

Other elements in 5zac:

The structure of Crystal Structure of Cona-R2M also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Cona-R2M (pdb code 5zac). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Cona-R2M, PDB code: 5zac:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5zac

Go back to Calcium Binding Sites List in 5zac
Calcium binding site 1 out of 6 in the Crystal Structure of Cona-R2M


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 Cona-R2M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:32.7
occ:1.00
 O A:TYR12 2.2 32.6 1.0
OD1 A:ASP10 2.2 25.4 1.0
O A:HOH417 2.3 5.4 1.0
OD2 A:ASP19 2.5 39.0 1.0
OD1 A:ASN14 2.7 27.8 1.0
OD2 A:ASP10 3.0 22.3 1.0
CG A:ASP10 3.0 23.5 1.0
C A:TYR12 3.4 31.3 1.0
CG A:ASP19 3.7 41.0 1.0
CG A:ASN14 3.8 29.4 1.0
N A:ASN14 3.9 28.0 1.0
OD1 A:ASP19 4.2 40.6 1.0
CB A:ASN14 4.3 28.0 1.0
MN A:MN301 4.3 43.8 1.0
CA A:TYR12 4.3 31.9 1.0
CA A:PRO13 4.4 30.5 1.0
O A:ASP208 4.4 20.0 1.0
N A:PRO13 4.4 31.5 1.0
N A:TYR12 4.4 29.4 1.0
CB A:TYR12 4.5 35.9 1.0
CB A:ASP10 4.5 22.8 1.0
C A:PRO13 4.5 29.5 1.0
O A:ARG228 4.6 20.9 1.0
OD2 A:ASP208 4.6 18.0 1.0
CA A:ASN14 4.7 28.4 1.0
CA A:ARG228 4.8 20.6 1.0
CB A:ARG228 4.8 20.6 1.0
CB A:ASP19 4.8 42.4 1.0
ND2 A:ASN14 4.9 29.1 1.0
CE1 A:HIS24 4.9 28.2 1.0

Calcium binding site 2 out of 6 in 5zac

Go back to Calcium Binding Sites List in 5zac
Calcium binding site 2 out of 6 in the Crystal Structure of Cona-R2M


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 Cona-R2M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:48.2
occ:1.00
 OE2 A:GLU122 2.9 56.8 1.0
OG1 B:THR49 3.6 30.3 1.0
CD A:GLU122 3.6 53.8 1.0
CD B:PRO68 3.6 26.4 1.0
N B:PRO68 3.7 27.1 1.0
O B:HOH429 3.7 27.2 1.0
CG B:PRO68 3.8 27.3 1.0
OE1 A:GLU122 4.0 58.5 1.0
CA B:PRO68 4.0 29.3 1.0
O A:SER117 4.1 38.6 1.0
O B:SER66 4.1 28.2 1.0
C B:TYR67 4.2 26.1 1.0
O A:HOH450 4.2 17.5 1.0
CB B:THR49 4.4 26.5 1.0
CB B:PRO68 4.5 27.7 1.0
CG A:GLU122 4.5 47.6 1.0
C B:SER66 4.7 24.6 1.0
O B:TYR67 4.7 26.1 1.0
CA B:TYR67 4.7 26.6 1.0
C A:SER117 4.9 37.4 1.0
N B:TYR67 4.9 25.4 1.0

Calcium binding site 3 out of 6 in 5zac

Go back to Calcium Binding Sites List in 5zac
Calcium binding site 3 out of 6 in the Crystal Structure of Cona-R2M


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 Cona-R2M within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:25.3
occ:1.00
 O B:TYR12 2.3 32.3 1.0
OD1 B:ASP10 2.3 18.2 1.0
O B:HOH411 2.4 13.3 1.0
OD1 B:ASN14 2.4 32.9 1.0
OD2 B:ASP19 2.5 35.1 1.0
CG B:ASP10 3.0 19.2 1.0
OD2 B:ASP10 3.1 19.2 1.0
CG B:ASN14 3.5 32.9 1.0
C B:TYR12 3.5 31.2 1.0
CG B:ASP19 3.6 37.9 1.0
N B:ASN14 3.7 32.2 1.0
CB B:ASN14 3.9 32.0 1.0
MN B:MN301 4.1 39.9 1.0
OD1 B:ASP19 4.2 41.8 1.0
CA B:PRO13 4.3 31.5 1.0
N B:PRO13 4.4 31.8 1.0
C B:PRO13 4.4 32.3 1.0
O B:ASP208 4.4 20.3 1.0
CA B:TYR12 4.4 29.5 1.0
CB B:ASP10 4.4 19.5 1.0
CA B:ASN14 4.4 32.4 1.0
N B:TYR12 4.5 26.0 1.0
CB B:TYR12 4.6 31.6 1.0
ND2 B:ASN14 4.6 33.4 1.0
CB B:ASP19 4.8 39.0 1.0
CB B:ARG228 4.8 26.1 1.0
CA B:ARG228 4.8 25.4 1.0
O B:HOH419 4.8 26.1 1.0
OD2 B:ASP208 4.9 22.4 1.0
CE1 B:HIS24 4.9 36.0 1.0
O B:ARG228 5.0 27.4 1.0

Calcium binding site 4 out of 6 in 5zac

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Calcium binding site 4 out of 6 in the Crystal Structure of Cona-R2M


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 Cona-R2M within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:33.2
occ:1.00
 OD1 C:ASP10 2.0 18.6 1.0
OD2 C:ASP19 2.2 25.6 1.0
O C:HOH417 2.3 8.2 1.0
OD1 C:ASN14 2.4 27.4 1.0
O C:TYR12 2.4 23.2 1.0
CG C:ASP10 2.8 19.9 1.0
OD2 C:ASP10 3.0 20.3 1.0
CG C:ASP19 3.3 30.6 1.0
CG C:ASN14 3.5 26.4 1.0
C C:TYR12 3.6 24.5 1.0
OD1 C:ASP19 3.7 30.1 1.0
MN C:MN301 4.1 35.7 1.0
N C:ASN14 4.1 24.3 1.0
CB C:ASN14 4.2 26.6 1.0
CB C:ASP10 4.2 21.2 1.0
N C:TYR12 4.3 25.8 1.0
CA C:TYR12 4.3 25.6 1.0
O C:ARG228 4.4 24.1 1.0
O C:ASP208 4.4 20.7 1.0
CB C:TYR12 4.4 28.0 1.0
CB C:ASP19 4.6 32.3 1.0
ND2 C:ASN14 4.6 27.5 1.0
N C:PRO13 4.6 25.0 1.0
CE1 C:HIS24 4.6 18.3 1.0
OD2 C:ASP208 4.7 20.2 1.0
CA C:ARG228 4.7 22.3 1.0
O C:HOH409 4.8 14.6 1.0
CA C:PRO13 4.8 25.3 1.0
CB C:ARG228 4.8 23.4 1.0
CA C:ASN14 4.8 25.8 1.0
CA C:ASP10 4.8 21.7 1.0
NE2 C:HIS24 4.9 18.2 1.0
C C:PRO13 4.9 23.8 1.0

Calcium binding site 5 out of 6 in 5zac

Go back to Calcium Binding Sites List in 5zac
Calcium binding site 5 out of 6 in the Crystal Structure of Cona-R2M


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 Cona-R2M within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:27.6
occ:1.00
 OD1 D:ASP10 2.1 16.4 1.0
O D:HOH418 2.2 12.4 1.0
OD2 D:ASP19 2.3 24.6 1.0
O D:TYR12 2.4 23.4 1.0
ND2 D:ASN14 2.7 28.6 1.0
O D:HOH401 2.8 30.2 1.0
CG D:ASP10 2.8 18.6 1.0
OD2 D:ASP10 2.8 19.1 1.0
CG D:ASP19 3.3 29.7 1.0
C D:TYR12 3.6 24.2 1.0
OD1 D:ASP19 3.7 28.1 1.0
CG D:ASN14 3.8 30.0 1.0
MN D:MN301 3.9 35.9 1.0
N D:ASN14 4.2 28.1 1.0
CB D:ASN14 4.2 30.4 1.0
O D:HOH422 4.3 11.5 1.0
CB D:ASP10 4.3 19.6 1.0
N D:TYR12 4.4 22.6 1.0
CA D:TYR12 4.4 23.3 1.0
CE1 D:HIS24 4.4 26.4 1.0
NE2 D:HIS24 4.5 26.3 1.0
O D:ARG228 4.5 24.8 1.0
O D:ASP208 4.6 22.6 1.0
CB D:ASP19 4.6 30.2 1.0
N D:PRO13 4.6 26.1 1.0
CA D:ARG228 4.7 24.6 1.0
CB D:TYR12 4.7 24.0 1.0
CB D:ARG228 4.7 26.7 1.0
CA D:PRO13 4.8 27.4 1.0
CA D:ASN14 4.8 29.4 1.0
OD1 D:ASN14 4.9 33.8 1.0
CA D:ASP10 4.9 20.2 1.0
OD2 D:ASP208 4.9 23.4 1.0
C D:PRO13 4.9 27.3 1.0

Calcium binding site 6 out of 6 in 5zac

Go back to Calcium Binding Sites List in 5zac
Calcium binding site 6 out of 6 in the Crystal Structure of Cona-R2M


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 Cona-R2M within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:40.0
occ:1.00
 OG1 D:THR49 3.2 29.8 1.0
NZ C:LYS116 3.8 42.5 1.0
N D:PRO68 4.0 35.0 1.0
CD D:PRO68 4.1 34.2 1.0
CG D:PRO68 4.1 33.9 1.0
CB D:THR49 4.1 27.4 1.0
CE C:LYS116 4.1 43.0 1.0
CG2 C:VAL187 4.1 34.0 1.0
OG D:SER66 4.2 27.5 1.0
CA D:PRO68 4.3 35.3 1.0
C D:TYR67 4.4 31.8 1.0
O D:HOH445 4.5 28.4 1.0
CB D:SER66 4.5 26.6 1.0
O D:SER66 4.5 23.2 1.0
CB D:PRO68 4.7 34.0 1.0
C D:SER66 4.7 24.3 1.0
N D:TYR67 4.8 26.9 1.0
CA D:TYR67 4.8 29.6 1.0
O D:TYR67 4.9 32.3 1.0
O D:HOH448 4.9 24.2 1.0

Reference:

R.T.Hu, G.Yang, H.M.Ding, J.B.Ma, Y.Q.Ma, J.H.Gan, G.S.Chen. Competition Between Supramolecular Interaction and Protein-Protein Interaction in Protein Crystallization:Effects of Crystallization Method and Small Molecular Bridge Ind Eng Chem Res V. 57 6726 2018.
ISSN: ISSN 0888-5885
DOI: 10.1021/ACS.IECR.8B00657
Page generated: Wed Jul 9 12:11:35 2025

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