Calcium in PDB 7y5n: Structure of 1:1 Papp-A.Prombp Complex(Half Map)

Enzymatic activity of Structure of 1:1 Papp-A.Prombp Complex(Half Map)

All present enzymatic activity of Structure of 1:1 Papp-A.Prombp Complex(Half Map):
3.4.24.79;

Other elements in 7y5n:

The structure of Structure of 1:1 Papp-A.Prombp Complex(Half Map) also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of 1:1 Papp-A.Prombp Complex(Half Map) (pdb code 7y5n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structure of 1:1 Papp-A.Prombp Complex(Half Map), PDB code: 7y5n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 7y5n

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Calcium binding site 1 out of 7 in the Structure of 1:1 Papp-A.Prombp Complex(Half Map)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of 1:1 Papp-A.Prombp Complex(Half Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1611

b:16.0
occ:1.00
 OD1 C:ASP785 2.6 26.9 1.0
O C:ASP785 2.6 26.9 1.0
O C:ARG678 2.7 24.2 1.0
OD1 C:ASP668 2.7 17.7 1.0
N C:ALA663 3.5 20.4 1.0
CG C:ASP785 3.6 26.9 1.0
C C:ASP785 3.7 26.9 1.0
CG C:ASP668 3.8 17.7 1.0
C C:ARG678 3.9 24.2 1.0
CA C:ALA663 4.1 20.4 1.0
CA C:ASP785 4.2 26.9 1.0
OD2 C:ASP668 4.2 17.7 1.0
O C:HIS666 4.3 18.8 1.0
OD2 C:ASP785 4.4 26.9 1.0
CB C:ARG678 4.5 24.2 1.0
CB C:ASP785 4.5 26.9 1.0
C C:GLU662 4.5 26.1 1.0
N C:ASP668 4.6 17.7 1.0
CA C:GLU662 4.6 26.1 1.0
CB C:GLU662 4.7 26.1 1.0
CD C:LYS455 4.7 20.6 1.0
CA C:ARG678 4.7 24.2 1.0
OE1 C:GLU662 4.7 26.1 1.0
N C:GLU664 4.7 22.7 1.0
NZ C:LYS455 4.8 20.6 1.0
N C:THR679 4.8 25.6 1.0
N C:ALA786 4.9 36.6 1.0
CA C:PRO667 4.9 21.4 1.0
CA C:THR679 4.9 25.6 1.0
C C:ALA663 4.9 20.4 1.0

Calcium binding site 2 out of 7 in 7y5n

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Calcium binding site 2 out of 7 in the Structure of 1:1 Papp-A.Prombp Complex(Half Map)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of 1:1 Papp-A.Prombp Complex(Half Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1612

b:60.2
occ:1.00
 OE1 C:GLU392 2.5 64.0 1.0
OD1 C:ASP389 2.6 55.8 1.0
O C:VAL376 2.8 65.8 1.0
CG C:ASP389 3.3 55.8 1.0
OD2 C:ASP389 3.4 55.8 1.0
OD2 C:ASP378 3.5 62.7 1.0
OD1 C:ASN374 3.5 70.4 1.0
CD C:GLU392 3.6 64.0 1.0
O C:ASN374 3.8 70.4 1.0
C C:VAL376 4.0 65.8 1.0
CG C:ASP378 4.0 62.7 1.0
OE2 C:GLU392 4.1 64.0 1.0
N C:ASN374 4.3 70.4 1.0
C C:ASN374 4.4 70.4 1.0
OD1 C:ASP378 4.4 62.7 1.0
N C:ASP378 4.6 62.7 1.0
CB C:ASP389 4.7 55.8 1.0
N C:VAL376 4.7 65.8 1.0
CG C:ASN374 4.7 70.4 1.0
CA C:CYS377 4.7 62.5 1.0
N C:CYS377 4.8 62.5 1.0
CB C:ASP378 4.8 62.7 1.0
C C:CYS377 4.9 62.5 1.0
C C:GLY375 4.9 66.3 1.0
O C:ASP389 4.9 55.8 1.0
CA C:ASN374 4.9 70.4 1.0
CG C:GLU392 4.9 64.0 1.0

Calcium binding site 3 out of 7 in 7y5n

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Calcium binding site 3 out of 7 in the Structure of 1:1 Papp-A.Prombp Complex(Half Map)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of 1:1 Papp-A.Prombp Complex(Half Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1613

b:37.9
occ:1.00
 O C:TYR866 2.5 31.4 1.0
O C:ILE871 2.5 36.2 1.0
OD2 C:ASP881 2.5 31.1 1.0
OE1 C:GLU878 2.6 32.8 1.0
OE2 C:GLU878 2.6 32.8 1.0
OD1 C:ASP869 2.8 34.5 1.0
CD C:GLU878 2.9 32.8 1.0
OE1 C:GLN873 2.9 35.1 1.0
OD2 C:ASP869 3.1 34.5 1.0
CD C:GLN873 3.1 35.1 1.0
CG C:ASP869 3.4 34.5 1.0
NE2 C:GLN873 3.6 35.1 1.0
C C:TYR866 3.7 31.4 1.0
CG C:ASP881 3.7 31.1 1.0
CG C:GLN873 3.7 35.1 1.0
C C:ILE871 3.7 36.2 1.0
N C:TYR866 3.9 31.4 1.0
CB C:GLN873 4.1 35.1 1.0
N C:GLN873 4.3 35.1 1.0
CA C:TYR866 4.4 31.4 1.0
CG C:GLU878 4.4 32.8 1.0
CB C:ASP881 4.5 31.1 1.0
OD1 C:ASP881 4.5 31.1 1.0
C C:GLY865 4.5 35.6 1.0
CA C:ILE871 4.5 36.2 1.0
N C:ILE871 4.5 36.2 1.0
CB C:ILE871 4.6 36.2 1.0
N C:CYS867 4.7 39.7 1.0
N C:ILE872 4.7 33.7 1.0
CA C:GLY865 4.7 35.6 1.0
CA C:ILE872 4.8 33.7 1.0
CA C:CYS867 4.8 39.7 1.0
C C:ILE872 4.8 33.7 1.0
CB C:ASP869 4.9 34.5 1.0
CA C:GLN873 4.9 35.1 1.0

Calcium binding site 4 out of 7 in 7y5n

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Calcium binding site 4 out of 7 in the Structure of 1:1 Papp-A.Prombp Complex(Half Map)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of 1:1 Papp-A.Prombp Complex(Half Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1614

b:22.8
occ:1.00
 OE1 C:GLU509 2.5 35.2 1.0
O C:THR523 2.5 25.2 1.0
OG1 C:THR523 2.5 25.2 1.0
O C:CYS520 2.6 22.6 1.0
OD1 C:ASP518 2.6 21.2 1.0
OE2 C:GLU509 3.1 35.2 1.0
CD C:GLU509 3.2 35.2 1.0
C C:THR523 3.6 25.2 1.0
C C:CYS520 3.8 22.6 1.0
CG C:ASP518 3.8 21.2 1.0
CB C:THR523 3.8 25.2 1.0
CA C:THR523 4.2 25.2 1.0
N C:CYS520 4.2 22.6 1.0
OD2 C:ASP518 4.3 21.2 1.0
O C:THR516 4.4 28.6 1.0
N C:THR523 4.4 25.2 1.0
CA C:CYS520 4.4 22.6 1.0
N C:ASP518 4.4 21.2 1.0
O C:SER513 4.6 31.6 1.0
CB C:CYS520 4.6 22.6 1.0
CG C:GLU509 4.7 35.2 1.0
N C:ASN524 4.8 27.7 1.0
N C:ASN521 4.9 32.0 1.0
CA C:PRO512 4.9 39.2 1.0
CG2 C:THR523 4.9 25.2 1.0
CB C:ASP518 4.9 21.2 1.0
C C:ASN524 4.9 27.7 1.0
N C:LEU519 4.9 20.0 1.0
N C:SER513 4.9 31.6 1.0

Calcium binding site 5 out of 7 in 7y5n

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Calcium binding site 5 out of 7 in the Structure of 1:1 Papp-A.Prombp Complex(Half Map)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of 1:1 Papp-A.Prombp Complex(Half Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1615

b:67.7
occ:1.00
 OE2 C:GLU923 2.5 53.1 1.0
OD2 C:ASP930 2.5 71.0 1.0
O C:VAL918 2.6 66.0 1.0
O C:HIS913 2.7 35.3 1.0
CB C:ASP916 3.0 57.6 1.0
OE1 C:GLU923 3.1 53.1 1.0
CD C:GLU923 3.2 53.1 1.0
CG C:ASP930 3.6 71.0 1.0
C C:VAL918 3.7 66.0 1.0
C C:HIS913 3.8 35.3 1.0
CG C:ASP916 3.8 57.6 1.0
OD2 C:ASP916 3.9 57.6 1.0
CA C:ASP916 4.0 57.6 1.0
CB C:ASP930 4.1 71.0 1.0
CA C:HIS913 4.2 35.3 1.0
CB C:HIS913 4.3 35.3 1.0
N C:ASP916 4.3 57.6 1.0
CG2 C:VAL918 4.3 66.0 1.0
C C:ASP916 4.4 57.6 1.0
N C:VAL918 4.4 66.0 1.0
N C:CYS919 4.6 67.4 1.0
CA C:VAL918 4.6 66.0 1.0
CG C:GLU923 4.6 53.1 1.0
N C:GLY917 4.7 70.3 1.0
CA C:CYS919 4.7 67.4 1.0
OD1 C:ASP930 4.7 71.0 1.0
OE2 C:GLU920 4.8 52.3 1.0
OD1 C:ASP916 4.9 57.6 1.0
O C:ASP916 4.9 57.6 1.0
N C:ASP914 4.9 44.5 1.0
CD2 C:HIS913 5.0 35.3 1.0

Calcium binding site 6 out of 7 in 7y5n

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Calcium binding site 6 out of 7 in the Structure of 1:1 Papp-A.Prombp Complex(Half Map)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of 1:1 Papp-A.Prombp Complex(Half Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1616

b:43.1
occ:1.00
 OD2 C:ASP356 2.5 45.6 1.0
OD1 C:ASP341 2.5 43.9 1.0
O C:ASN343 2.6 44.3 1.0
OD2 C:ASP345 2.7 50.0 1.0
O C:LYS338 2.7 40.5 1.0
CG C:ASP356 3.0 45.6 1.0
OD1 C:ASP356 3.1 45.6 1.0
O C:ASP341 3.3 43.9 1.0
CG C:ASP341 3.5 43.9 1.0
CG C:ASP345 3.6 50.0 1.0
OD1 C:ASN343 3.7 44.3 1.0
C C:LYS338 3.8 40.5 1.0
C C:ASN343 3.8 44.3 1.0
O C:ILE339 3.8 40.2 1.0
N C:ASP345 3.9 50.0 1.0
OD2 C:ASP341 4.0 43.9 1.0
CB C:ASP345 4.1 50.0 1.0
C C:ASP341 4.2 43.9 1.0
C C:ILE339 4.3 40.2 1.0
CB C:ASP356 4.4 45.6 1.0
N C:ASP341 4.4 43.9 1.0
CG C:ASN343 4.5 44.3 1.0
CB C:ASP359 4.5 52.4 1.0
CA C:ILE339 4.5 40.2 1.0
CA C:CYS344 4.6 50.2 1.0
OD1 C:ASP345 4.6 50.0 1.0
N C:ILE339 4.6 40.2 1.0
O C:ASP356 4.6 45.6 1.0
CB C:ASP341 4.6 43.9 1.0
N C:CYS344 4.6 50.2 1.0
CA C:ASP341 4.6 43.9 1.0
CA C:ASP345 4.6 50.0 1.0
C C:CYS344 4.7 50.2 1.0
N C:ASN343 4.7 44.3 1.0
CA C:LYS338 4.7 40.5 1.0
CA C:ASN343 4.8 44.3 1.0
CB C:LYS338 4.9 40.5 1.0

Calcium binding site 7 out of 7 in 7y5n

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Calcium binding site 7 out of 7 in the Structure of 1:1 Papp-A.Prombp Complex(Half Map)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of 1:1 Papp-A.Prombp Complex(Half Map) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1617

b:23.7
occ:1.00
 O C:CYS891 2.5 30.1 1.0
OD1 C:ASN884 2.5 23.3 1.0
O C:ILE886 2.5 23.9 1.0
ND2 C:ASN884 2.6 23.3 1.0
CG C:ASN884 2.9 23.3 1.0
C C:CYS891 3.6 30.1 1.0
C C:ILE886 3.6 23.9 1.0
N C:ILE886 3.7 23.9 1.0
O C:SER892 4.1 27.7 1.0
CA C:ILE886 4.2 23.9 1.0
CB C:ASN884 4.3 23.3 1.0
C C:SER892 4.3 27.7 1.0
CB C:ASP882 4.3 28.4 1.0
CB C:ASP889 4.3 26.2 1.0
CB C:CYS891 4.4 30.1 1.0
N C:LYS885 4.4 21.5 1.0
CA C:CYS891 4.4 30.1 1.0
CG C:ASP889 4.5 26.2 1.0
OD2 C:ASP889 4.6 26.2 1.0
N C:SER892 4.6 27.7 1.0
CB C:ILE886 4.7 23.9 1.0
N C:CYS891 4.7 30.1 1.0
CA C:SER892 4.7 27.7 1.0
C C:LYS885 4.7 21.5 1.0
N C:ASN887 4.8 26.2 1.0
OD2 C:ASP882 4.8 28.4 1.0
CA C:LYS885 4.8 21.5 1.0
N C:LEU893 4.9 20.9 1.0
CG C:ASP882 5.0 28.4 1.0

Reference:

Q.Zhong, H.Chu, G.Wang, C.Zhang, R.Li, F.Guo, X.Meng, X.Lei, Y.Zhou, R.Ren, L.Tao, N.Li, N.Gao, Y.Wei, J.Qiao, J.Hang. Structural Insights Into the Covalent Regulation of Papp-A Activity By Prombp and STC2. Cell Discov V. 8 137 2022.
ISSN: ESSN 2056-5968
PubMed: 36550107
DOI: 10.1038/S41421-022-00502-2
Page generated: Tue Apr 4 19:15:27 2023

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