Zinc in PDB 8adl: Cryo-Em Structure of the Sea Complex

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 28;

Binding sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the Sea Complex (pdb code 8adl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 28 binding sites of Zinc where determined in the Cryo-Em Structure of the Sea Complex, PDB code: 8adl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1201 b:124.3 occ:1.00 ND1 C:HIS1120 2.1 88.3 1.0 SG C:CYS1101 2.3 103.5 1.0 SG C:CYS1123 2.3 83.3 1.0 SG C:CYS1098 2.3 62.3 1.0 CB C:CYS1098 2.9 68.0 1.0 CE1 C:HIS1120 3.1 82.5 1.0 CG C:HIS1120 3.1 88.2 1.0 CB C:CYS1123 3.4 87.5 1.0 CB C:HIS1120 3.4 84.9 1.0 CB C:CYS1101 3.5 83.7 1.0 N C:CYS1101 3.9 87.6 1.0 N C:HIS1120 4.0 84.7 1.0 NE2 C:HIS1120 4.2 79.3 1.0 CD2 C:HIS1120 4.2 82.8 1.0 CA C:CYS1101 4.3 78.5 1.0 CA C:HIS1120 4.3 81.0 1.0 CA C:CYS1098 4.4 67.7 1.0 CB C:TYR1100 4.5 63.1 1.0 CA C:CYS1123 4.8 84.4 1.0 C C:TYR1100 4.8 79.6 1.0 N C:TYR1100 4.9 66.6 1.0 C C:CYS1098 5.0 73.0 1.0 CA C:TYR1100 5.0 69.0 1.0

Zinc binding site 2 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1202 b:128.2 occ:1.00 SG C:CYS1142 2.3 104.1 1.0 SG C:CYS1115 2.3 96.8 1.0 SG C:CYS1112 2.3 108.6 1.0 SG C:CYS1140 2.3 116.6 1.0 CB C:CYS1112 3.2 89.7 1.0 CB C:CYS1140 3.3 102.0 1.0 CB C:CYS1115 3.4 87.6 1.0 N C:CYS1115 3.6 82.0 1.0 CB C:CYS1142 3.6 90.5 1.0 CA C:CYS1142 3.9 86.2 1.0 CA C:CYS1115 4.0 82.0 1.0 O C:CYS1115 4.0 91.7 1.0 ZN C:ZN1203 4.2 137.8 1.0 N C:CYS1142 4.2 89.1 1.0 O C:CYS1140 4.3 106.4 1.0 C C:CYS1115 4.4 85.7 1.0 C C:CYS1140 4.5 103.0 1.0 CA C:CYS1140 4.5 103.2 1.0 CA C:CYS1112 4.6 85.0 1.0 CB C:ASN1114 4.7 88.8 1.0 C C:ASN1114 4.7 90.8 1.0 N C:ASN1114 4.8 95.0 1.0 CB C:CYS1134 4.8 75.0 1.0 O C:MET1145 4.9 100.8 1.0 C C:ASN1141 4.9 101.1 1.0 CA C:ASN1114 5.0 90.0 1.0

Zinc binding site 3 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1203 b:137.8 occ:1.00 ND1 C:HIS1117 2.1 82.5 1.0 SG C:CYS1138 2.3 130.7 1.0 SG C:CYS1134 2.3 77.6 1.0 SG C:CYS1115 2.3 96.8 1.0 CE1 C:HIS1117 2.8 79.2 1.0 CB C:CYS1134 3.0 75.0 1.0 CB C:CYS1115 3.1 87.6 1.0 CG C:HIS1117 3.2 84.2 1.0 OG C:SER1136 3.5 94.7 1.0 CB C:HIS1117 3.7 81.7 1.0 CB C:CYS1138 3.8 111.1 1.0 NE2 C:HIS1117 4.0 79.8 1.0 ZN C:ZN1202 4.2 128.2 1.0 CD2 C:HIS1117 4.2 79.7 1.0 CB C:CYS1140 4.4 102.0 1.0 CA C:CYS1115 4.5 82.0 1.0 CA C:CYS1134 4.5 77.0 1.0 SG C:CYS1142 4.6 104.1 1.0 C C:CYS1115 4.8 85.7 1.0 N C:CYS1138 4.9 105.5 1.0 CB C:SER1136 4.9 90.3 1.0 CA C:CYS1138 4.9 106.5 1.0

Zinc binding site 4 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1101 b:156.2 occ:1.00 ND1 G:HIS1016 2.0 77.5 1.0 ND1 G:HIS1013 2.0 97.4 1.0 SG G:CYS956 2.3 105.0 1.0 SG G:CYS953 2.3 96.0 1.0 CE1 G:HIS1016 2.3 78.4 1.0 CB G:CYS953 2.7 76.4 1.0 CE1 G:HIS1013 2.8 92.2 1.0 CG G:HIS1013 3.2 94.0 1.0 CG G:HIS1016 3.4 78.9 1.0 NE2 G:HIS1016 3.6 77.5 1.0 CB G:HIS1013 3.7 93.1 1.0 CB G:CYS956 3.8 91.8 1.0 N G:CYS956 4.0 92.5 1.0 NE2 G:HIS1013 4.0 88.8 1.0 N G:HIS1013 4.1 87.9 1.0 CD2 G:HIS1016 4.1 80.8 1.0 CB G:HIS1016 4.2 79.2 1.0 CA G:CYS953 4.2 75.0 1.0 CD2 G:HIS1013 4.2 91.9 1.0 CA G:CYS956 4.4 89.7 1.0 CA G:HIS1013 4.5 86.7 1.0 C G:CYS953 4.9 82.7 1.0 CB G:MET958 4.9 79.2 1.0 CB G:ILE955 4.9 72.2 1.0 O G:MET958 4.9 97.1 1.0 C G:CYS956 5.0 83.9 1.0 N G:MET958 5.0 91.0 1.0

Zinc binding site 5 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1102 b:170.4 occ:1.00 SG G:CYS881 2.3 125.7 1.0 SG G:CYS943 2.3 109.3 1.0 SG G:CYS884 2.3 125.0 1.0 SG G:CYS946 2.3 125.1 1.0 CB G:CYS884 3.4 118.4 1.0 CB G:CYS943 3.4 102.0 1.0 CB G:CYS946 3.5 118.7 1.0 N G:CYS884 3.6 113.7 1.0 CB G:CYS881 3.8 124.9 1.0 N G:CYS946 3.8 116.7 1.0 CA G:CYS884 4.0 117.4 1.0 CA G:CYS946 4.2 117.2 1.0 C G:ASN883 4.5 123.4 1.0 CB G:ASN883 4.5 124.6 1.0 C G:HIS945 4.5 112.5 1.0 CB G:HIS945 4.6 112.5 1.0 C G:CYS884 4.7 117.3 1.0 N G:LYS885 4.8 105.3 1.0 CA G:CYS943 4.9 106.0 1.0 N G:HIS945 4.9 109.8 1.0 CA G:ASN883 4.9 124.5 1.0 CA G:HIS945 4.9 111.6 1.0 C G:CYS946 4.9 113.6 1.0 N G:ASN883 5.0 126.0 1.0

Zinc binding site 6 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1103 b:122.4 occ:1.00 SG G:CYS1008 2.3 85.4 1.0 SG G:CYS1036 2.3 82.4 1.0 SG G:CYS1005 2.3 96.3 1.0 SG G:CYS1034 2.3 104.8 1.0 CB G:CYS1005 3.1 83.4 1.0 CB G:CYS1034 3.3 90.4 1.0 CB G:CYS1008 3.5 79.9 1.0 CB G:CYS1036 3.7 81.9 1.0 N G:CYS1008 3.8 84.3 1.0 O G:CYS1034 4.0 92.5 1.0 ZN G:ZN1104 4.2 134.3 1.0 CA G:CYS1036 4.2 83.0 1.0 CA G:CYS1008 4.3 80.3 1.0 C G:CYS1034 4.4 89.8 1.0 CB G:SER1007 4.4 77.9 1.0 N G:CYS1036 4.5 82.5 1.0 CA G:CYS1034 4.5 89.7 1.0 CA G:CYS1005 4.5 76.7 1.0 CG C:ARG1107 4.6 75.2 1.0 C G:SER1007 4.7 83.4 1.0 N G:SER1007 4.8 87.0 1.0 CA G:SER1007 4.9 78.0 1.0 CB G:CYS1027 5.0 62.6 1.0

Zinc binding site 7 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1104 b:134.3 occ:1.00 ND1 G:HIS1010 2.1 63.2 1.0 SG G:CYS1008 2.3 85.4 1.0 SG G:CYS1032 2.3 115.0 1.0 SG G:CYS1027 2.3 60.9 1.0 CB G:CYS1008 2.6 79.9 1.0 CE1 G:HIS1010 2.9 62.1 1.0 CB G:CYS1032 3.1 92.8 1.0 CB G:CYS1027 3.1 62.6 1.0 CG G:HIS1010 3.1 74.0 1.0 CB G:HIS1010 3.6 72.4 1.0 OG1 G:THR1029 3.7 89.7 1.0 CA G:CYS1008 3.9 80.3 1.0 NE2 G:HIS1010 4.0 61.2 1.0 O G:CYS1008 4.1 84.5 1.0 CD2 G:HIS1010 4.2 71.1 1.0 C G:CYS1008 4.2 78.4 1.0 ZN G:ZN1103 4.2 122.4 1.0 CB G:CYS1034 4.4 90.4 1.0 CA G:CYS1032 4.6 88.5 1.0 CA G:CYS1027 4.6 56.9 1.0 N G:HIS1010 4.6 62.7 1.0 CA G:HIS1010 4.7 64.5 1.0 N G:CYS1008 4.9 84.3 1.0 SG G:CYS1036 5.0 82.4 1.0 CB G:THR1029 5.0 82.3 1.0

Zinc binding site 8 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1401 b:164.8 occ:1.00 ND1 A:HIS1315 2.1 83.2 1.0 SG A:CYS1296 2.3 94.4 1.0 SG A:CYS1293 2.3 77.7 1.0 SG A:CYS1318 2.3 80.7 1.0 CE1 A:HIS1315 2.7 75.8 1.0 CB A:CYS1293 3.0 66.6 1.0 CG A:HIS1315 3.2 74.0 1.0 CB A:CYS1318 3.4 84.2 1.0 CB A:CYS1296 3.5 74.7 1.0 CB A:HIS1315 3.8 76.9 1.0 NE2 A:HIS1315 3.8 65.8 1.0 N A:CYS1296 4.0 76.8 1.0 N A:HIS1315 4.1 66.3 1.0 CD2 A:HIS1315 4.1 67.2 1.0 CA A:CYS1296 4.3 68.2 1.0 CA A:CYS1293 4.5 59.4 1.0 CA A:HIS1315 4.6 73.4 1.0 CA A:CYS1318 4.8 83.1 1.0 CB A:LEU1295 4.9 60.4 1.0

Zinc binding site 9 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1402 b:149.9 occ:1.00 SG A:CYS1283 2.3 88.7 1.0 SG A:CYS1246 2.3 92.8 1.0 SG A:CYS1249 2.3 76.4 1.0 SG A:CYS1286 2.3 101.2 1.0 CB A:CYS1283 2.9 76.5 1.0 CB A:CYS1246 3.0 90.3 1.0 CB A:CYS1286 3.3 90.4 1.0 CB A:CYS1249 3.6 77.8 1.0 N A:CYS1286 3.9 92.8 1.0 N A:CYS1249 4.1 77.3 1.0 CA A:CYS1286 4.2 91.0 1.0 CA A:CYS1283 4.4 74.0 1.0 CA A:CYS1249 4.4 78.5 1.0 CA A:CYS1246 4.5 86.1 1.0 CD1 A:ILE1253 4.7 71.9 1.0 CB A:SER1285 4.9 88.6 1.0 C A:CYS1286 4.9 92.1 1.0 CB A:ARG1248 4.9 89.5 1.0 CB A:LYS1288 4.9 69.8 1.0 C A:SER1285 5.0 88.7 1.0 C A:CYS1283 5.0 85.7 1.0

Zinc binding site 10 out of 28 in the Cryo-Em Structure of the Sea Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cryo-Em Structure of the Sea Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1403 b:122.2 occ:1.00 ND1 A:HIS1312 2.1 71.0 1.0 SG A:CYS1310 2.3 91.3 1.0 SG A:CYS1331 2.3 89.6 1.0 SG A:CYS1335 2.3 106.6 1.0 CE1 A:HIS1312 2.4 63.2 1.0 CB A:CYS1310 2.9 69.9 1.0 CB A:CYS1331 3.0 73.6 1.0 CG A:HIS1312 3.3 70.9 1.0 NE2 A:HIS1312 3.7 62.8 1.0 CB A:CYS1335 3.8 94.0 1.0 CD2 A:HIS1312 4.1 69.0 1.0 CB A:HIS1312 4.1 69.7 1.0 CA A:CYS1310 4.3 71.0 1.0 CA A:CYS1331 4.5 75.8 1.0 C A:CYS1310 4.5 73.1 1.0 O A:CYS1310 4.6 75.6 1.0 CA A:CYS1335 5.0 88.7 1.0 N A:GLY1333 5.0 63.8 1.0

L.Tafur, K.Hinterndorfer, C.Gabus, C.Lamanna, A.Bergmann, Y.Sadian, F.Hamdi, F.L.Kyrilis, P.L.Kastritis, R.Loewith. Cryo-Em Structure of the Sea Complex. Nature V. 611 399 2022.
ISSN: ESSN 1476-4687
PubMed: 36289347
DOI: 10.1038/S41586-022-05370-0